@article {pmid37228449, year = {2023}, author = {Schmidt, P and Koch, TJ and Blessing, MA and Karakostis, FA and Harvati, K and Dresely, V and Charrié-Duhaut, A}, title = {Production method of the Königsaue birch tar documents cumulative culture in Neanderthals.}, journal = {Archaeological and anthropological sciences}, volume = {15}, number = {6}, pages = {84}, doi = {10.1007/s12520-023-01789-2}, pmid = {37228449}, issn = {1866-9557}, abstract = {UNLABELLED: Birch tar is the oldest synthetic substance made by early humans. The earliest such artefacts are associated with Neanderthals. According to traditional interpretations, their study allows understanding Neanderthal tool behaviours, skills and cultural evolution. However, recent work has found that birch tar can also be produced with simple processes, or even result from fortuitous accidents. Even though these findings suggest that birch tar per se is not a proxy for cognition, they do not shed light on the process by which Neanderthals produced it, and, therefore, cannot evaluate the implications of that behaviour. Here, we address the question of how tar was made by Neanderthals. Through a comparative chemical analysis of the two exceptional birch tar pieces from Königsaue (Germany) and a large reference birch tar collection made with Stone Age techniques, we found that Neanderthals did not use the simplest method to make tar. Rather, they distilled tar in an intentionally created underground environment that restricted oxygen flow and remained invisible during the process. This degree of complexity is unlikely to have been invented spontaneously. Our results suggest that Neanderthals invented or developed this process based on previous simpler methods and constitute one of the clearest indicators of cumulative cultural evolution in the European Middle Palaeolithic.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12520-023-01789-2.}, }
@article {pmid37220274, year = {2023}, author = {Tobler, R and Souilmi, Y and Huber, CD and Bean, N and Turney, CSM and Grey, ST and Cooper, A}, title = {The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {22}, pages = {e2213061120}, doi = {10.1073/pnas.2213061120}, pmid = {37220274}, issn = {1091-6490}, abstract = {The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.}, }
@article {pmid37202264, year = {2023}, author = {Klein, K and Weniger, GC and Ludwig, P and Stepanek, C and Zhang, X and Wegener, C and Shao, Y}, title = {Assessing climatic impact on transition from Neanderthal to anatomically modern human population on Iberian Peninsula: a macroscopic perspective.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2023.04.025}, pmid = {37202264}, issn = {2095-9281}, abstract = {The Iberian Peninsula is of particular interest for the research on the Neanderthal (NEA) to anatomically modern human (AMH) population transition. The AMHs arrived in Iberia last from Eastern Europe and thus any possible contacts between the two populations occurred here later than elsewhere. The transition process took place in the earlier part of the Marine Isotope Stage 3 (∼60-27 cal ka BP) as repeated and profound climate changes challenged the population stability. To investigate how climate change and population interactions influenced the transition, we combine climate data with archaeological-site data to reconstruct the Human Existence Potential, a measure of the probability of human existence, for both the NEA and AMH populations in the Greenland Interstadial 11-10 (GI11-10) and Stadial 10-9/Heinrich event 4 (GS10-9/HE4) times. It is found that during GS10-9/HE4, large parts of the peninsula became unsuitable for NEA human existence and the NEA settlement areas contracted to isolated coastal hot spots. As a consequence, the NEA networks became highly unstable, triggering the final collapse of the population. The AMHs arrived in Iberia in GI10 but were confined to patches in the northern most strip of the peninsula. They were soon facing the much colder climate of GS10-9/HE4, which prevented their further expansion or even caused a contraction of their settlement areas. Thus, due to the constellation of climate change and the dispersal of the two populations into different regions of the peninsula, it is unlikely that the NEAs and AMHs coexisted in extensive areas and the AMHs had a significant influence on the demography of the NEAs.}, }
@article {pmid37196358, year = {2023}, author = {Cobat, A and Zhang, Q and Covid Human Genetic Effort,  and Abel, L and Casanova, JL and Fellay, J}, title = {Human Genomics of COVID-19 Pneumonia: Contributions of Rare and Common Variants.}, journal = {Annual review of biomedical data science}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-biodatasci-020222-021705}, pmid = {37196358}, issn = {2574-3414}, abstract = {SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection is silent or benign in most infected individuals, but causes hypoxemic COVID-19 pneumonia in about 10% of cases. We review studies of the human genetics of life-threatening COVID-19 pneumonia, focusing on both rare and common variants. Large-scale genome-wide association studies have identified more than 20 common loci robustly associated with COVID-19 pneumonia with modest effect sizes, some implicating genes expressed in the lungs or leukocytes. The most robust association, on chromosome 3, concerns a haplotype inherited from Neanderthals. Sequencing studies focusing on rare variants with a strong effect have been particularly successful, identifying inborn errors of type I interferon (IFN) immunity in 1-5% of unvaccinated patients with critical pneumonia, and their autoimmune phenocopy, autoantibodies against type I IFN, in another 15-20% of cases. Our growing understanding of the impact of human genetic variation on immunity to SARS-CoV-2 is enabling health systems to improve protection for individuals and populations. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 6 is August 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid37192163, year = {2023}, author = {Rong, S and Neil, CR and Welch, A and Duan, C and Maguire, S and Meremikwu, IC and Meyerson, M and Evans, BJ and Fairbrother, WG}, title = {Large-scale functional screen identifies genetic variants with splicing effects in modern and archaic humans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {21}, pages = {e2218308120}, doi = {10.1073/pnas.2218308120}, pmid = {37192163}, issn = {1091-6490}, support = {R01 GM127472/GM/NIGMS NIH HHS/United States ; }, abstract = {Humans coexisted and interbred with other hominins which later became extinct. These archaic hominins are known to us only through fossil records and for two cases, genome sequences. Here, we engineer Neanderthal and Denisovan sequences into thousands of artificial genes to reconstruct the pre-mRNA processing patterns of these extinct populations. Of the 5,169 alleles tested in this massively parallel splicing reporter assay (MaPSy), we report 962 exonic splicing mutations that correspond to differences in exon recognition between extant and extinct hominins. Using MaPSy splicing variants, predicted splicing variants, and splicing quantitative trait loci, we show that splice-disrupting variants experienced greater purifying selection in anatomically modern humans than that in Neanderthals. Adaptively introgressed variants were enriched for moderate-effect splicing variants, consistent with positive selection for alternative spliced alleles following introgression. As particularly compelling examples, we characterized a unique tissue-specific alternative splicing variant at the adaptively introgressed innate immunity gene TLR1, as well as a unique Neanderthal introgressed alternative splicing variant in the gene HSPG2 that encodes perlecan. We further identified potentially pathogenic splicing variants found only in Neanderthals and Denisovans in genes related to sperm maturation and immunity. Finally, we found splicing variants that may contribute to variation among modern humans in total bilirubin, balding, hemoglobin levels, and lung capacity. Our findings provide unique insights into natural selection acting on splicing in human evolution and demonstrate how functional assays can be used to identify candidate causal variants underlying differences in gene regulation and phenotype.}, }
@article {pmid37156940, year = {2023}, author = {Li, Q and Chen, J and Faux, P and Delgado, ME and Bonfante, B and Fuentes-Guajardo, M and Mendoza-Revilla, J and Chacón-Duque, JC and Hurtado, M and Villegas, V and Granja, V and Jaramillo, C and Arias, W and Barquera, R and Everardo-Martínez, P and Sánchez-Quinto, M and Gómez-Valdés, J and Villamil-Ramírez, H and Silva de Cerqueira, CC and Hünemeier, T and Ramallo, V and Wu, S and Du, S and Giardina, A and Paria, SS and Khokan, MR and Gonzalez-José, R and Schüler-Faccini, L and Bortolini, MC and Acuña-Alonzo, V and Canizales-Quinteros, S and Gallo, C and Poletti, G and Rojas, W and Rothhammer, F and Navarro, N and Wang, S and Adhikari, K and Ruiz-Linares, A}, title = {Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {481}, pmid = {37156940}, issn = {2399-3642}, abstract = {We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10[-8]) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.}, }
@article {pmid37155903, year = {2023}, author = {Linscott, B and Pike, AWG and Angelucci, DE and Cooper, MJ and Milton, JS and Matias, H and Zilhão, J}, title = {Reconstructing Middle and Upper Paleolithic human mobility in Portuguese Estremadura through laser ablation strontium isotope analysis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {20}, pages = {e2204501120}, doi = {10.1073/pnas.2204501120}, pmid = {37155903}, issn = {1091-6490}, abstract = {Understanding mobility and landscape use is important in reconstructing subsistence behavior, range, and group size, and it may contribute to our understanding of phenomena such as the dynamics of biological and cultural interactions between distinct populations of Upper Pleistocene humans. However, studies using traditional strontium isotope analysis are generally limited to identifying locations of childhood residence or nonlocal individuals and lack the sampling resolution to detect movement over short timescales. Here, using an optimized methodology, we present highly spatially resolved [87]Sr/[86]Sr measurements made by laser ablation multicollector inductively coupled plasma mass spectrometry along the growth axis of the enamel of two marine isotope stage 5b, Middle Paleolithic Neanderthal teeth (Gruta da Oliveira), a Tardiglacial, Late Magdalenian human tooth (Galeria da Cisterna), and associated contemporaneous fauna from the Almonda karst system, Torres Novas, Portugal. Strontium isotope mapping of the region shows extreme variation in [87]Sr/[86]Sr, with values ranging from 0.7080 to 0.7160 over a distance of c. 50 km, allowing short-distance (and arguably short-duration) movement to be detected. We find that the early Middle Paleolithic individuals roamed across a subsistence territory of approximately 600 km[2], while the Late Magdalenian individual parsimoniously fits a pattern of limited, probably seasonal movement along the right bank of the 20-km-long Almonda River valley, between mouth and spring, exploiting a smaller territory of approximately 300 km[2]. We argue that the differences in territory size are due to an increase in population density during the Late Upper Paleolithic.}, }
@article {pmid37142741, year = {2023}, author = {Brand, CM and Colbran, LL and Capra, JA}, title = {Resurrecting the alternative splicing landscape of archaic hominins using machine learning.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {37142741}, issn = {2397-334X}, abstract = {Alternative splicing contributes to adaptation and divergence in many species. However, it has not been possible to directly compare splicing between modern and archaic hominins. Here, we unmask the recent evolution of this previously unobservable regulatory mechanism by applying SpliceAI, a machine-learning algorithm that identifies splice-altering variants (SAVs), to high-coverage genomes from three Neanderthals and a Denisovan. We discover 5,950 putative archaic SAVs, of which 2,186 are archaic-specific and 3,607 also occur in modern humans via introgression (244) or shared ancestry (3,520). Archaic-specific SAVs are enriched in genes that contribute to traits potentially relevant to hominin phenotypic divergence, such as the epidermis, respiration and spinal rigidity. Compared to shared SAVs, archaic-specific SAVs occur in sites under weaker selection and are more common in genes with tissue-specific expression. Further underscoring the importance of negative selection on SAVs, Neanderthal lineages with low effective population sizes are enriched for SAVs compared to Denisovan and shared SAVs. Finally, we find that nearly all introgressed SAVs in humans were shared across the three Neanderthals, suggesting that older SAVs were more tolerated in human genomes. Our results reveal the splicing landscape of archaic hominins and identify potential contributions of splicing to phenotypic differences among hominins.}, }
@article {pmid37141315, year = {2023}, author = {Klapper, M and Hübner, A and Ibrahim, A and Wasmuth, I and Borry, M and Haensch, VG and Zhang, S and Al-Jammal, WK and Suma, H and Fellows Yates, JA and Frangenberg, J and Velsko, IM and Chowdhury, S and Herbst, R and Bratovanov, EV and Dahse, HM and Horch, T and Hertweck, C and González Morales, MR and Straus, LG and Vilotijevic, I and Warinner, C and Stallforth, P}, title = {Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic.}, journal = {Science (New York, N.Y.)}, volume = {}, number = {}, pages = {eadf5300}, doi = {10.1126/science.adf5300}, pmid = {37141315}, issn = {1095-9203}, abstract = {Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.}, }
@article {pmid37134082, year = {2023}, author = {Slimak, L}, title = {The three waves: Rethinking the structure of the first Upper Paleolithic in Western Eurasia.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0277444}, doi = {10.1371/journal.pone.0277444}, pmid = {37134082}, issn = {1932-6203}, abstract = {The Neronian is a lithic tradition recognized in the Middle Rhône Valley of Mediterranean France now directly linked to Homo sapiens and securely dated to 54,000 years ago (ka), pushing back the arrival of modern humans in Europe by 10 ka. This incursion of modern humans into Neandertal territory and the relationships evoked between the Neronian and the Levantine Initial Upper Paleolithic (IUP) question the validity of concepts that define the first H. sapiens migrations and the very nature of the first Upper Paleolithic in western Eurasia. Direct comparative analyses between lithic technology from Grotte Mandrin and East Mediterranean archeological sequences, especially Ksar Akil, suggest that the three key phases of the earliest Levantine Upper Paleolithic have very precise technical and chronological counterparts in Western Europe, recognized from the Rhône Valley to Franco-Cantabria. These trans-Mediterranean technical connections suggest three distinct waves of H. sapiens expansion into Europe between 55-42 ka. These elements support an original thesis on the origin, structure, and evolution of the first moments of the Upper Paleolithic in Europe tracing parallel archaeological changes in the East Mediterranean region and Europe.}, }
@article {pmid37114314, year = {2022}, author = {Benítez-Burraco, A and Torres-Ruiz, R and Gelabert, P and Lalueza-Fox, C and Rodríguez-Perales, S and García-Bellido, P}, title = {Human-specific changes in two functional enhancers of FOXP2.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {68}, number = {11}, pages = {16-19}, doi = {10.14715/cmb/2022.68.11.3}, pmid = {37114314}, issn = {1165-158X}, abstract = {FOXP2 is a gene involved in language development and function. Neanderthals and humans share the same coding region of the gene, although the formers are thought to have exhibited less sophisticated language abilities. In this paper, we report on several human-specific changes in two functional enhancers of FOXP2. Two of these variants are located within the binding sites for the transcription factors POLR2A and SMARCC1, respectively. Interestingly, SMARCC1 is involved in brain development and vitamin D metabolism. We hypothesize that the human specific change in this position might have resulted in a different regulation pattern of FOXP2 expression in our species compared to extinct hominins, with a potential impact on our language abilities.}, }
@article {pmid37103242, year = {2023}, author = {Witt, KE and Funk, A and Añorve-Garibay, V and Lopez Fang, L and Huerta-Sanchez, E}, title = {The impact of modern admixture on archaic human ancestry in human populations.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evad066}, pmid = {37103242}, issn = {1759-6653}, abstract = {Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, which have shaped genetic ancestry in modern humans. For example, populations in the Americas are often mosaics of different ancestries due to recent admixture events as part of European colonization. Admixed individuals also often have introgressed DNA from Neanderthals and Denisovans that may have come from multiple ancestral populations, which may affect how archaic ancestry is distributed across an admixed genome. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual's archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight enrichment of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.}, }
@article {pmid37100851, year = {2023}, author = {Ríos, L and Sleeper, MM and Danforth, MD and Murphy, HW and Kutinsky, I and Rosas, A and Bastir, M and Gómez-Cambronero, J and Sanjurjo, R and Campens, L and Rider, O and Pastor, F}, title = {The aorta in humans and African great apes, and cardiac output and metabolic levels in human evolution.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6841}, pmid = {37100851}, issn = {2045-2322}, abstract = {Humans have a larger energy budget than great apes, allowing the combination of the metabolically expensive traits that define our life history. This budget is ultimately related to the cardiac output, the product of the blood pumped from the ventricle and the number of heart beats per minute, a measure of the blood available for the whole organism physiological activity. To show the relationship between cardiac output and energy expenditure in hominid evolution, we study a surrogate measure of cardiac output, the aortic root diameter, in humans and great apes. When compared to gorillas and chimpanzees, humans present an increased body mass adjusted aortic root diameter. We also use data from the literature to show that over the human lifespan, cardiac output and total energy expenditure follow almost identical trajectories, with a marked increase during the period of brain growth, and a plateau during most of the adult life. The limited variation of adjusted cardiac output with sex, age and physical activity supports the compensation model of energy expenditure in humans. Finally, we present a first study of cardiac output in the skeleton through the study of the aortic impression in the vertebral bodies of the spine. It is absent in great apes, and present in humans and Neanderthals, large-brained hominins with an extended life cycle. An increased adjusted cardiac output, underlying higher total energy expenditure, would have been a key process in human evolution.}, }
@article {pmid37091460, year = {2023}, author = {Sinaei, R and Pezeshki, S and Sinaei, R}, title = {What Kept Back on the Mirror of COVID-19-Related Acute Transverse Myelitis? A Genetic Background!.}, journal = {Iranian journal of child neurology}, volume = {17}, number = {2}, pages = {143-147}, pmid = {37091460}, issn = {1735-4668}, abstract = {COVID-19-associated acute transverse myelitis (ATM) cases have been reported worldwide. Nevertheless, Iran, Italy, and the USA are the most affected countries, witnessing the possibility that genetic factors might be associated with this susceptibility. The genetic variants of the coronavirus-2 entry mechanisms and host innate immune response-related genes like interferons, interleukins, Toll-like receptors, human leukocyte antigens, blood groups, and some risk loci may be accountable. This study describes the compatibility of the geographical distribution between ATM and the Neanderthal core haplotype that confers risk for severe COVID-19 and some possible culprit genes.}, }
@article {pmid37070424, year = {2023}, author = {Gómez-Olivencia, A and Arsuaga, JL}, title = {The Sima de los Huesos cervical spine.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.25224}, pmid = {37070424}, issn = {1932-8494}, abstract = {Information regarding the evolution of the neck in genus Homo is hampered owing to a limited fossil record. Neandertals display significant metric and/or morphological differences in all the cervical vertebrae, when compared to Homo sapiens. Thus, the important fossil record from the Middle Pleistocene site of Sima de los Huesos (SH) not only offers important information about the evolution of this anatomical region within the Neandertal lineage, but also provides important clues to understand the evolution of this region at the genus level. We present the current knowledge of the anatomy of the cervical spine of the hominins found in SH compared to that of Neandertals and modern humans, and, when possible, to Homo erectus and Homo antecessor. The current SH fossil record comprises 172 cervical specimens (after refittings) belonging to a minimum of 11 atlases, 13 axes, and 52 subaxial cervical vertebrae. The SH hominins exhibit a morphological pattern in their cervical spine more similar to that of Neandertals than that of H. sapiens, which is consistent with the phylogenetic position of these hominins. However, there are some differences between the SH hominins and Neandertals in this anatomical region, primarily in the length and robusticity, and to a lesser extent in the orientation of the spinous processes of the lowermost cervical vertebrae. We hypothesize that these differences in the lowermost subaxial cervical vertebrae could be related to the increase in the brain size and/or changes in the morphology of the skull that occurred in the Neandertal lineage.}, }
@article {pmid36882431, year = {2023}, author = {Marín-Arroyo, AB and Terlato, G and Vidal-Cordasco, M and Peresani, M}, title = {Subsistence of early anatomically modern humans in Europe as evidenced in the Protoaurignacian occupations of Fumane Cave, Italy.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3788}, pmid = {36882431}, issn = {2045-2322}, support = {818299/ERC_/European Research Council/International ; }, mesh = {Animals ; Humans ; Adaptation, Psychological ; Caves ; Europe ; Goats ; Italy ; *Rupicapra ; *Neanderthals ; }, abstract = {Documenting the subsistence strategies developed by early modern humans is relevant for understanding the success of their dispersal throughout Eurasia. Today, we know that there was not a single colonization event and that the process was progressive while coping with the MIS3 abrupt climatic oscillations. Modern humans expanded into the continent by adapting to different topographic situations and by exploiting resources in diverse ecological niches. The northern part of Italy is one of the first European regions where early modern humans are documented. Here, we present the subsistence regimen adopted by the Protoaurignacian groups in two different levels in Fumane Cave based on archaeozoological data. New radiocarbon dates confirm an overlap between Uluzzian and Protoaurignacian occupations, around 42 and 41,000 cal BP, and reveal that modern humans occupied the cave from GI10 to GS9, the last level coinciding with the Heinrich Event 4. The data indicate seasonal site occupations during late spring/summer and that prey exploitation was focused mostly on ibex and chamois, killed in nearby areas. The whole faunal assemblage suggests the presence of early modern humans in a cold environment with mostly open landscapes and patchy woodlands. The estimation of net primary productivity (NPP) in Fumane, compared with other contemporaneous Italian sites, reflects how the NPP fluctuations in the Prealpine area, where Fumane is located, affected the biotic resources in contrast to known Mediterranean sites. From a pan-European perspective, the spatiotemporal fluctuation of the NPP versus the subsistence strategies adopted by Protoaurignacian groups in the continent supports rapid Homo sapiens dispersal and resilience in a mosaic of environments that were affected by significant climate changes.}, }
@article {pmid37053172, year = {2023}, author = {Doronicheva, EV and Golovanova, LV and Doronichev, VB and Kurbanov, RN}, title = {Archaeological evidence for two culture diverse Neanderthal populations in the North Caucasus and contacts between them.}, journal = {PloS one}, volume = {18}, number = {4}, pages = {e0284093}, doi = {10.1371/journal.pone.0284093}, pmid = {37053172}, issn = {1932-6203}, abstract = {Neanderthals were widespread during the Middle Palaeolithic (MP) across Europe and Asia, including the Caucasus Mountains. Occupying the border between eastern Europe and West Asia, the Caucasus is important region regarding the Neanderthal occupation of Eurasia. On current radiometric estimates, the MP is represented in the Caucasus between about 260-210 ka and about 40 ka. Archaeological record indicates that several culture diverse MP hominin populations inhabited the Caucasus, but the region complex population history during this period remains poorly understood. In this paper, we identify for the first time the archaeological evidence indicating contacts between two culture diverse MP Neanderthal populations in the North Caucasus and discuss the nature of these contacts. Basing on the lithic assemblages that we excavated at Mezmaiskaya cave in the north-western Caucasus (Kuban River basin) and Saradj-Chuko grotto in the north-central Caucasus (Terek River basin), dating from MIS 5 to MIS 3, and comparative data from other MP sites in the Caucasus, we identify two large cultural regions that existed during the late MP in the North Caucasus. The distinctive toolkits and stone knapping technologies indicate that the MP assemblages from Mezmaiskaya cave and other sites in the west of North Caucasus represent a Caucasian variant of the Eastern Micoquian industry that was wide spread in central and eastern Europe, while the assemblages from Saradj-Chuko Grotto and other sites in the east of North Caucasus closely resemble the Zagros Mousterian industry that was wide spread in the Armenian Highlands, Lesser Caucasus and Zagros Mountains. The archaeological evidence implies that two culture diverse populations of Neanderthals settled the North Caucasus during the Late Pleistocene from two various source regions: from the Armenian Highlands and Lesser Caucasus along the Caspian Sea coast, and from Russian plain along the Sea of Azov coast.}, }
@article {pmid37035790, year = {2023}, author = {Chung, S and Son, JW}, title = {How Well Do We Understand Autistic Savant Artists: A Review of Various Hypotheses and Research Findings to Date.}, journal = {Soa--ch'ongsonyon chongsin uihak = Journal of child &amp; adolescent psychiatry}, volume = {34}, number = {2}, pages = {93-111}, pmid = {37035790}, issn = {1225-729X}, abstract = {The authors investigated the artistic characteristics of autistic savant artists, hypotheses on the proximate and ultimate causes of their emergence, recent psychological and other studies about them, and psychological and neuroaesthetic studies about non-savant autistic individuals. The artistic features of autistic savant artists were significantly similar to those of outsider artists. Furthermore, the authors investigated the explanatory power of the paradoxical functional facilitation theory, the superior visual perception hypothesis, the "Hmmmmm" hypothesis, and the Neanderthal theory of autism regarding the emergence of autistic savant artists. In addition, we investigated whether an increase in savant characteristics was related to a decrease in the ability for social communication. The authors suggested that in studies on the aesthetic experience of non-savant autistic individuals, their aesthetic experience ability is never lower than that of neurotypical individuals and that some non-savant autistic individuals may potentially have artistic talent. Finally, the authors reviewed the effectiveness of the "autism savant spectrum syndromic disorder" proposed by some researchers. More scientific and systematic studies on autistic savant artists from a multidisciplinary perspective are warranted.}, }
@article {pmid37016656, year = {2023}, author = {Turner, MD}, title = {Possible Causes of Hypertrophic Osteoarthropathy in the La Ferrassie 1 Neanderthal.}, journal = {Cureus}, volume = {15}, number = {3}, pages = {e35721}, pmid = {37016656}, issn = {2168-8184}, abstract = {For over a century, researchers have been perplexed by the unique osteological findings on La Ferrassie 1 (LF1), one of the most complete Neanderthal remains ever found. In 1997, Fennel and Trinkaus proposed that LF1 suffered from hypertrophic osteoarthropathy (HOA), likely secondary to chronic thoracic infection or pulmonary malignancy. This disease process can have many etiologies, and no study has fully explored the possible origin of LF1's HOA. Ultimately, it is most likely that LF1's HOA etiology arose from one of the many infectious diseases that prehistoric Neanderthals were exposed to, specifically a chronic pulmonary RNA virus.}, }
@article {pmid37010952, year = {2023}, author = {Richards, GD and Jabbour, RS and Guipert, G and Defleur, A}, title = {Neanderthal child's maxilla from Baume Moula-Guercy (Soyons, Ardèche, France).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.25218}, pmid = {37010952}, issn = {1932-8494}, abstract = {This article provides an ontogenetically-based comparative description of the Guercy 3 partial child's maxilla with Rdm[2] -RM[1] and unerupted RI[2] -RP[4] from Baume Moula-Guercy (MIS 5e) and examines its affinities to European and Middle Eastern Middle-to-Late Pleistocene (≈MIS 14-MIS 1) Homo. Description of the Guercy 3 maxilla and dentition (7.0 year ± 0.9 month) is based on observations of original fossils, casts, CT scans, literature descriptions, and virtual reconstructions. Our ontogenetic sample comprises a Preneanderthal-Neanderthal group and a Homo sapiens group. These groups are subdivided into (1) Preneanderthals (≈MIS 14-9), Early Neanderthals (MIS 7-5e), and Late Neanderthals (MIS 5d-3), and (2) Middle (MIS 5), Upper (MIS 3-2), and Late Upper Paleolithic (≈MIS 1), and recent H. sapiens. Standard techniques were employed for measurements and developmental age determinations.The Guercy 3 maxilla lacks changes found in Late Neanderthals, including the positioning of the root of the zygomatic process, infraorbital and nasal plates, premaxilla, buccal and labial alveolus, maxillary sinus, nasal cavity, and verticality of anterior tooth implantation. The morphology of the Guercy 3 maxilla more closely approximates that of Sima de los Huesos Preneanderthals, while the dentition more closely approximates the Early-Late Neanderthal condition. Maxillary remains of children and juveniles between MIS 14-MIS 5e are rare, and the available sample is fragmentary and distorted. Although fragmentary, the Guercy 3 maxilla is undistorted and provides new insights into the evolution of the midface in Neanderthals.}, }
@article {pmid37001690, year = {2023}, author = {Pomeroy, E}, title = {Review: The different adaptive trajectories in Neanderthals and Homo sapiens and their implications for contemporary human physiological variation.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {}, number = {}, pages = {111420}, doi = {10.1016/j.cbpa.2023.111420}, pmid = {37001690}, issn = {1531-4332}, abstract = {Neanderthals are our one of our closest evolutionary cousins, but while they evolved in Eurasia, we (anatomically modern humans, AMH) originated in Africa. This contrasting evolutionary history has led to morphological and genetic distinctions between our species. Neanderthals are characterised by a relatively stocky build, high body mass, proportionally wide bodies and shorter limbs, a bell-shaped ribcage with a wide pelvis, and a long, low cranial vault compared with AMH. Classic readings of Neanderthal morphology link many of these traits to cold climate adaptations, however these interpretations have been questioned and alternative hypotheses including behavioural factors, dietary adaptations, locomotor specialisations, evolutionary history and neutral evolutionary processes have been invoked. Compared with AMH, Neanderthals may have been adapted for strength and power rather than endurance and may have consumed a diet high in animal products. However, reviewing these hypotheses highlights a number of limitations in our understanding of contemporary human physiology and metabolism, including the relationship between climate and morphology in AMH and Neanderthals, physiological limits on protein consumption, and the relationship between gut morphology and diet. As various relevant factors are clearly linked (e.g. diet, behaviour, metabolism, morphology, activity), ultimately a more integrated approach may be needed to fully understand Neanderthal biology. Variation among contemporary AMHs may offer, with caveats, a useful model for understanding the evolution of both Neanderthal and modern human characteristics, which in turn may further deepen our understanding of variability within and between contemporary humans. Neanderthals; Anatomically modern humans; morphology; climate adaptation; power adaptations; metabolism; diet; physiology; endurance running.}, }
@article {pmid36998196, year = {2023}, author = {Quam, R and Martínez, I and Rak, Y and Hylander, B and Pantoja, A and Lorenzo, C and Conde-Valverde, M and Keeling, B and Ortega Martínez, MC and Arsuaga, JL}, title = {The Neandertal nature of the Atapuerca Sima de los Huesos mandibles.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.25190}, pmid = {36998196}, issn = {1932-8494}, abstract = {The recovery of additional mandibular fossils from the Atapuerca Sima de los Huesos (SH) site provides new insights into the evolutionary significance of this sample. In particular, morphological descriptions of the new adult specimens are provided, along with standardized metric data and phylogenetically relevant morphological features for the expanded adult sample. The new and more complete specimens extend the known range of variation in the Atapuerca (SH) mandibles in some metric and morphological details. In other aspects, the addition of new specimens has made it possible to confirm previous observations based on more limited evidence. Pairwise comparisons of individual metric variables revealed the only significant difference between the Atapuerca (SH) hominins and Neandertals was a more vertical symphysis in the latter. Similarly, principal components analysis of size-adjusted variables showed a strong similarity between the Atapuerca (SH) hominins and Neandertals. Morphologically, the Atapuerca (SH) mandibles show nearly the full complement of Neandertal-derived features. Nevertheless, the Neandertals differ from the Atapuerca (SH) mandibles in showing a high frequency of the H/O mandibular foramen, a truncated, thinned and inverted gonial margin, a high placement of the mylohyoid line at the level of the M3, a more vertical symphysis and somewhat more pronounced expression of the chin structures. Size-related morphological variation in the SH hominins includes larger retromolar spaces, more posterior placement of the lateral corpus structures, and stronger markings associated with the muscles of mastication in larger specimens. However, phylogenetically relevant features in the SH sample are fairly stable and do not vary with the overall size of the mandible. Direct comparison of the enlarged mandibular sample from Atapuerca (SH) with the Mauer mandible, the type specimen of H. heidelbergensis, reveals important differences from the SH hominins, and there is no morphological counterpart of Mauer within the SH sample, suggesting the SH fossils should not be assigned to this taxon. The Atapuerca (SH) mandibles show a greater number of derived Neandertal features, particularly those related to midfacial prognathism and in the configuration of the superior ramus, than other European middle Pleistocene specimens. This suggests that more than one evolutionary lineage co-existed in the middle Pleistocene, and, broadly speaking, it appears possible to separate the European middle Pleistocene mandibular remains into two distinct groupings. One group shows a suite of derived Neandertal features and includes specimens from the sites of Atapuerca (SH), Payre, l'Aubesier and Ehringsdorf. The other group includes specimens that generally lack derived Neandertal features and includes the mandibles from the sites of Mauer, Mala Balanica, Montmaurin and (probably) Visogliano. The two published Arago mandibles differ strongly from one another, with Arago 2 probably belonging to this former group, and Neandertal affinities being more difficult to identify in Arago 13. Outside of the SH sample, derived Neandertal features in the mandible only become more common during the second half of the middle Pleistocene. Acceptance of a cladogenetic pattern of evolution during the European middle Pleistocene has the potential to reconcile the predictions of the accretion model and the two phases model for the appearance of Neandertal morphology. The precise taxonomic classification of the SH hominins must contemplate features from the dentition, cranium, mandible and postcranial skeleton, all of which are preserved at the SH site. Nevertheless, the origin of the Neandertal clade may be tied to a speciation event reflected in the appearance of a suite of derived Neandertal features in the face, dentition and mandible, all of which are present in the Atapuerca (SH) hominins. This same suite of features also provides a useful anatomical basis to include other European middle Pleistocene mandibles and crania within the Neandertal clade.}, }
@article {pmid36980999, year = {2023}, author = {Toncheva, D and Marinova, M and Chobanov, T and Serbezov, D}, title = {Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/genes14030727}, pmid = {36980999}, issn = {2073-4425}, abstract = {Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.}, }
@article {pmid36979362, year = {2023}, author = {Xiao, F and Li, J and Lagniton, PNP and Kou, SH and Lei, H and Tam, B and Wang, SM}, title = {Evolutionary Origin of MUTYH Germline Pathogenic Variations in Modern Humans.}, journal = {Biomolecules}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/biom13030429}, pmid = {36979362}, issn = {2218-273X}, abstract = {MUTYH plays an essential role in preventing oxidation-caused DNA damage. Pathogenic germline variations in MUTYH damage its function, causing intestinal polyposis and colorectal cancer. Determination of the evolutionary origin of the variation is essential to understanding the etiological relationship between MUTYH variation and cancer development. In this study, we analyzed the origins of pathogenic germline variants in human MUTYH. Using a phylogenic approach, we searched MUTYH pathogenic variants in modern humans in the MUTYH of 99 vertebrates across eight clades. We did not find pathogenic variants shared between modern humans and the non-human vertebrates following the evolutionary tree, ruling out the possibility of cross-species conservation as the origin of human pathogenic variants in MUTYH. We then searched the variants in the MUTYH of 5031 ancient humans and extinct Neanderthals and Denisovans. We identified 24 pathogenic variants in 42 ancient humans dated between 30,570 and 480 years before present (BP), and three pathogenic variants in Neanderthals dated between 65,000 and 38,310 years BP. Data from our study revealed that human MUTYH pathogenic variants mostly arose in recent human history and partially originated from Neanderthals.}, }
@article {pmid36966596, year = {2023}, author = {Zhang, Y and Li, Z}, title = {Three-dimensional geometric morphometric study of the Xuchang 2 cranium.}, journal = {Journal of human evolution}, volume = {178}, number = {}, pages = {103347}, doi = {10.1016/j.jhevol.2023.103347}, pmid = {36966596}, issn = {1095-8606}, abstract = {Results of traditional metric and nonmetric assessments suggest that the Xuchang hominin shares features with Neanderthals. To comprehensively compare the nuchal morphology of XC 2 to those of the genus Homo, we conduct a three-dimensional geometric morphometric study with 35 cranial landmarks and surface semilandmarks of XC 2, Homo erectus, Middle Pleistocene humans, Neanderthals, and early and recent modern humans. Results reveal that the centroid size of XC 2 is larger than that of early and recent modern humans and can only be compared to that of Middle Pleistocene humans and H. erectus. Early and recent modern humans share a nuchal morphology distinct from archaic hominins (Ngandong H. erectus, Middle Pleistocene humans, and Neanderthals), except for SM 3, Sangiran 17, and Asian and African H. erectus. Although Ngandong specimens differ from the other H. erectus, it is unclear whether this represents a temporal or spatial trend in the process of evolution of this species. The nuchal morphological resemblance between Middle Pleistocene humans and Neanderthals may be attributed to similar cranial architecture and cerebellar shape. The great nuchal morphological variation shared by recent modern humans may indicate a particular developmental pattern. In conclusion, the nuchal morphology of different human groups is highly variable and may be caused by different factors including brain globularization and developmental plasticity. XC 2 shares similar nuchal morphology with Middle Pleistocene humans and Neanderthals, but these results are insufficient to fully resolve the taxonomic status of XC 2.}, }
@article {pmid36964200, year = {2023}, author = {Profico, A and Buzi, C and Di Vincenzo, F and Boggioni, M and Borsato, A and Boschian, G and Marchi, D and Micheli, M and Cecchi, JM and Samadelli, M and Tafuri, MA and Arsuaga, JL and Manzi, G}, title = {Virtual excavation and analysis of the early Neanderthal cranium from Altamura (Italy).}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {316}, pmid = {36964200}, issn = {2399-3642}, abstract = {Complete Neanderthal skeletons are almost unique findings. A very well-preserved specimen of this kind was discovered in 1993 in the deepest recesses of a karstic system near the town of Altamura in Southern Italy. We present here a detailed description of the cranium, after we virtually extracted it from the surrounding stalagmites and stalactites. The morphology of the Altamura cranium fits within the Neanderthal variability, though it retains features occurring in more archaic European samples. Some of these features were never observed in Homo neanderthalensis, i.e. in fossil specimens dated between 300 and 40 ka. Considering the U-Th age we previously obtained (>130 ka), the morphology of Altamura suggests that the archaic traits it retains may have been originated by geographic isolation of the early Neanderthal populations from Southern Italy.}, }
@article {pmid36950386, year = {2023}, author = {Skov, L and Coll Macià, M and Lucotte, EA and Cavassim, MIA and Castellano, D and Schierup, MH and Munch, K}, title = {Extraordinary selection on the human X chromosome associated with archaic admixture.}, journal = {Cell genomics}, volume = {3}, number = {3}, pages = {100274}, pmid = {36950386}, issn = {2666-979X}, abstract = {The X chromosome in non-African humans shows less diversity and less Neanderthal introgression than expected from neutral evolution. Analyzing 162 human male X chromosomes worldwide, we identified fourteen chromosomal regions where nearly identical haplotypes spanning several hundred kilobases are found at high frequencies in non-Africans. Genetic drift alone cannot explain the existence of these haplotypes, which must have been associated with strong positive selection in partial selective sweeps. Moreover, the swept haplotypes are entirely devoid of archaic ancestry as opposed to the non-swept haplotypes in the same genomic regions. The ancient Ust'-Ishim male dated at 45,000 before the present (BP) also carries the swept haplotypes, implying that selection on the haplotypes must have occurred between 45,000 and 55,000 years ago. Finally, we find that the chromosomal positions of sweeps overlap previously reported hotspots of selective sweeps in great ape evolution, suggesting a mechanism of selection unique to X chromosomes.}, }
@article {pmid36939312, year = {2023}, author = {Wei, X and Robles, CR and Pazokitoroudi, A and Ganna, A and Gusev, A and Durvasula, A and Gazal, S and Loh, PR and Reich, D and Sankararaman, S}, title = {The lingering effects of Neanderthal introgression on human complex traits.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, doi = {10.7554/eLife.80757}, pmid = {36939312}, issn = {2050-084X}, support = {GM100233/NH/NIH HHS/United States ; HG006399/NH/NIH HHS/United States ; R35GM125055/NH/NIH HHS/United States ; }, abstract = {The genetic variants introduced into the ancestors of modern humans from interbreeding with Neanderthals have been suggested to contribute an unexpected extent to complex human traits. However, testing this hypothesis has been challenging due to the idiosyncratic population genetic properties of introgressed variants. We developed rigorous methods to assess the contribution of introgressed Neanderthal variants to heritable trait variation relative to that of modern human variants. We applied these methods to analyze 235,592 introgressed Neanderthal variants and 96 distinct phenotypes measured in about 300,000 unrelated white British individuals in the UK Biobank. Introgressed Neanderthal variants have a significant contribution to trait variation consistent with the polygenic architecture of complex phenotypes (contributing 0.12% of heritable variation averaged across phenotypes). However, the contribution of introgressed variants tends to be significantly depleted relative to modern human variants matched for allele frequency and linkage disequilibrium (about 59% depletion on average), consistent with purifying selection on introgressed variants. Different from previous studies (McArthur 2021), we find no evidence for elevated heritability across the phenotypes examined. We identified 348 independent significant associations of introgressed Neanderthal variants with 64 phenotypes . Previous work (Skov 2020) has suggested that a majority of such associations are likely driven by statistical association with nearby modern human variants that are the true causal variants. We therefore developed a customized statistical fine-mapping methodology for introgressed variants that led us to identify 112 regions (at a false discovery proportion of 16%) across 47 phenotypes containing 4,303 unique genetic variants where introgressed variants are highly likely to have a phenotypic effect. Examination of these variants reveal their substantial impact on genes that are important for the immune system, development, and metabolism. Our results provide the first rigorous basis for understanding how Neanderthal introgression modulates complex trait variation in present-day humans.}, }
@article {pmid36932194, year = {2023}, author = {Avni, HL and Shvalb, N and Pokhojaev, A and Francis, S and Pelleg-Kallevag, R and Roul, V and Hublin, JJ and Rühli, F and May, H}, title = {Evolutionary roots of the risk of hip fracture in humans.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {283}, pmid = {36932194}, issn = {2399-3642}, abstract = {The transition to bipedal locomotion was a fundamental milestone in human evolution. Consequently, the human skeleton underwent substantial morphological adaptations. These adaptations are responsible for many of today's common physical impairments, including hip fractures. This study aims to reveal the morphological changes in the proximal femur, which increase the risk of intracapsular hip fractures in present-day populations. Our sample includes chimpanzees, early hominins, early Homo Neanderthals, as well as prehistoric and recent humans. Using Geometric Morphometric methods, we demonstrate differences in the proximal femur shape between hominids and populations that practiced different lifestyles. We show that the proximal femur morphology is a risk factor for intracapsular hip fracture independent of osteoporosis. Changes in the proximal femur, such as the shortening of the femoral neck and an increased anterolateral expansion of the greater trochanter, are associated with an increased risk for intracapsular hip fractures. We conclude that intracapsular hip fractures are a trade-off for efficient bipedal walking in humans, and their risk is exacerbated by reduced physical activity.}, }
@article {pmid36925053, year = {2023}, author = {Chen, Z and Reynolds, RH and Pardiñas, AF and Gagliano Taliun, SA and van Rheenen, W and Lin, K and Shatunov, A and Gustavsson, EK and Fogh, I and Jones, AR and Robberecht, W and Corcia, P and Chiò, A and Shaw, PJ and Morrison, KE and Veldink, JH and van den Berg, LH and Shaw, CE and Powell, JF and Silani, V and Hardy, JA and Houlden, H and Owen, MJ and Turner, MR and Ryten, M and Al-Chalabi, A}, title = {The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases.}, journal = {Neurobiology of disease}, volume = {}, number = {}, pages = {106082}, doi = {10.1016/j.nbd.2023.106082}, pmid = {36925053}, issn = {1095-953X}, abstract = {Humans are thought to be more susceptible to neurodegeneration than equivalently-aged primates. It is not known whether this vulnerability is specific to anatomically-modern humans or shared with other hominids. The contribution of introgressed Neanderthal DNA to neurodegenerative disorders remains uncertain. It is also unclear how common variants associated with neurodegenerative disease risk are maintained by natural selection in the population despite their deleterious effects. In this study, we aimed to quantify the genome-wide contribution of Neanderthal introgression and positive selection to the heritability of complex neurodegenerative disorders to address these questions. We used stratified-linkage disequilibrium score regression to investigate the relationship between five SNP-based signatures of natural selection, reflecting different timepoints of evolution, and genome-wide associated variants of the three most prevalent neurodegenerative disorders: Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease . We found no evidence for enrichment of positively-selected SNPs in the heritability of Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease, suggesting that common deleterious disease variants are unlikely to be maintained by positive selection. There was no enrichment of Neanderthal introgression in the SNP-heritability of these disorders, suggesting that Neanderthal admixture is unlikely to have contributed to disease risk. These findings provide insight into the origins of neurodegenerative disorders within the evolution of Homo sapiens and addresses a long-standing debate, showing that Neanderthal admixture is unlikely to have contributed to common genetic risk of neurodegeneration in anatomically-modern humans.}, }
@article {pmid36916962, year = {2023}, author = {Carretero, JM and García-González, R and Rodríguez, L and Arsuaga, JL}, title = {Main anatomical characteristics of the hominin fossil humeri from the Sima de los Huesos Middle Pleistocene site, Sierra de Atapuerca, Burgos, Spain: An update.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.25194}, pmid = {36916962}, issn = {1932-8494}, abstract = {Some of the Sima de los Huesos (SH) humeri have been previously studied and described elsewhere. Here we present an updated inventory and a review of the specimens recovered to the present day. The morphological key traits of the adult and subadult specimens are described, discussed, and illustrated. The SH humeri share with Neandertals many traits usually considered to be Neandertal specializations, thus, most of this morphological pattern is not exclusive to them. The variation found within fossil samples stresses the frequential nature of all these traits and in the specific case of the SH humeri, most of the traits considered as phylogenetically relevant are retained by their descendants, the Neandertals. Some traits are plesiomorphic for the entire genus Homo or are present in European hominins since the early Pleistocene. Finally, some other traits display high variability within the SH sample or different hominin samples and are of uncertain phylogenetic value. Altogether, this evidence is consistent with the hypothesis based on the overall cranial and postcranial morphology that the SH hominins are a sister group to the later Neandertals.}, }
@article {pmid36735645, year = {2023}, author = {Dekker, J and Larson, T and Tzvetkov, J and Harvey, VL and Dowle, A and Hagan, R and Genever, P and Schrader, S and Soressi, M and Hendy, J}, title = {Spatial analysis of the ancient proteome of archeological teeth using mass spectrometry imaging.}, journal = {Rapid communications in mass spectrometry : RCM}, volume = {37}, number = {8}, pages = {e9486}, doi = {10.1002/rcm.9486}, pmid = {36735645}, issn = {1097-0231}, abstract = {RATIONALE: Proteins extracted from archaeological bone and teeth are utilised for investigating the phylogeny of extinct and extant species, the biological sex and age of past individuals, as well as ancient health and physiology. However, variable preservation of proteins in archaeological materials represents a major challenge.<br><br>METHODS: To better understand the spatial distribution of ancient proteins preserved within teeth, we applied matrix assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for the first time to bioarchaeological samples to visualise the intensity of proteins in archaeological teeth thin sections. We specifically explored the spatial distribution of four proteins (collagen type I, of which&#xa0;the chains alpha-1 and alpha-2, alpha-2-HS-glycoprotein, haemoglobin subunit alpha and myosin light polypeptide 6).<br><br>RESULTS: We successfully identified ancient proteins in archaeological teeth thin sections using mass spectrometry imaging. The data are available via ProteomeXchange with identifier PXD038114. However, we observed that peptides did not always follow our hypotheses for their spatial distribution, with distinct differences observed in the spatial distribution of several proteins, and occasionally between peptides of the same protein.<br><br>CONCLUSIONS: While it remains unclear what causes these differences in protein intensity distribution within teeth, as revealed by MALDI-MSI in this study, we have demonstrated that MALDI-MSI can be successfully applied to mineralised bioarchaeological tissues to detect ancient peptides. In future applications, this technique could be particularly fruitful not just for understanding the preservation of proteins in a range of archaeological materials, but making informed decisions on sampling strategies and the targeting of key proteins of archaeological and biological interest.}, }
@article {pmid36893252, year = {2023}, author = {Herai, RH and Semendeferi, K and Muotri, AR}, title = {Comment on "Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals".}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6636}, pages = {eadf0602}, doi = {10.1126/science.adf0602}, pmid = {36893252}, issn = {1095-9203}, abstract = {Pinson et al. (1) concluded that the modern human TKTL1 gene is responsible for an increased number of cortical neurons. We show that the "putative Neanderthal variant" of TKTL1 is present in modern human backgrounds. We dispute their argument that this genetic variant is responsible for brain differences in modern humans as opposed to Neanderthals.}, }
@article {pmid36893240, year = {2023}, author = {Pinson, A and Maricic, T and Zeberg, H and Pääbo, S and Huttner, WB}, title = {Response to Comment on "Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals".}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6636}, pages = {eadf2212}, doi = {10.1126/science.adf2212}, pmid = {36893240}, issn = {1095-9203}, abstract = {Herai et al. discuss the known fact that a low percentage of modern humans who lack any overt phenotypes carry the ancestral TKTL1 allele. Our paper demonstrates that the amino acid substitution in TKTL1 increases neural progenitor cells and neurogenesis in the developing brain. It is another question if, and to what extent, this has consequences for the adult brain.}, }
@article {pmid36871458, year = {2023}, author = {Jones, EL and Carvalho, M}, title = {Ecospaces of the Middle to Upper Paleolithic transition: The archaeofaunal record of the Iberian Peninsula.}, journal = {Journal of human evolution}, volume = {177}, number = {}, pages = {103331}, doi = {10.1016/j.jhevol.2023.103331}, pmid = {36871458}, issn = {1095-8606}, abstract = {The rich archaeofaunal record of Iberia provides a means of exploring potential differences between Neanderthal and anatomically modern human interactions with the environment. In this article, we present an analysis of Iberian archaeofaunas dating between 60 and 30 ka to explore if, how, and why the faunal ecospaces of Neanderthals and anatomically modern humans differed. We test for impacts of chronology (as a proxy for Neanderthal and anatomically modern human exploitation) and environmental regionalization (using bioclimatic regions) on archaeofaunal composition, using a combination of cluster (unweighted pair-group method using arithmetic averages) and nonmetric multidimensional scaling. Our chronological analysis finds no significant compositional difference between Neanderthal and anatomically modern mammalian faunal assemblages; however, bioclimatic regionalization is stronger in anatomically modern human-affiliated assemblages than in Neanderthal ones, a finding that may indicate a difference in site occupation duration or foraging mobility between Neanderthals and anatomically modern humans.}, }
@article {pmid36857333, year = {2023}, author = {Shoaee, MJ and Breeze, PS and Drake, NA and Hashemi, SM and Vahdati Nasab, H and Breitenbach, SFM and Stevens, T and Boivin, N and Petraglia, MD}, title = {Defining paleoclimatic routes and opportunities for hominin dispersals across Iran.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0281872}, doi = {10.1371/journal.pone.0281872}, pmid = {36857333}, issn = {1932-6203}, abstract = {Fossil and archaeological evidence indicates that hominin dispersals into Southwest Asia occurred throughout the Pleistocene, including the expansion of Homo sapiens populations out of Africa. While there is evidence for hominin occupations in the Pleistocene in Iran, as evidenced by the presence of Lower to Upper Paleolithic archaeological sites, the extent to which humid periods facilitated population expansions into western Asia has remained unclear. To test the role of humid periods on hominin dispersals here we assess Paleolithic site distributions and paleoenvironmental records across Iran. We developed the first spatially comprehensive, high-resolution paleohydrological model for Iran in order to assess water availability and its influence on hominin dispersals. We highlight environmentally mediated routes which likely played a key role in Late Pleistocene hominin dispersals, including the expansion of H. sapiens and Neanderthals eastwards into Asia. Our combined analyses indicate that, during MIS 5, there were opportunities for hominins to traverse a northern route through the Alborz and Kopet Dagh Mountains and the Dasht-I Kavir desert owing to the presence of activated fresh water sources. We recognize a new southern route along the Zagros Mountains and extending eastwards towards Pakistan and Afghanistan. We find evidence for a potential northern route during MIS 3, which would have permitted hominin movements and species interactions in Southwest Asia. Between humid periods, these interconnections would have waned, isolating populations in the Zagros and Alborz Mountains, where hominins may have continued to have had access to water.}, }
@article {pmid36841571, year = {2023}, author = {Ganapathee, DS and Gunz, P}, title = {Insights into brain evolution through the genotype-phenotype connection.}, journal = {Progress in brain research}, volume = {275}, number = {}, pages = {73-92}, doi = {10.1016/bs.pbr.2022.12.013}, pmid = {36841571}, issn = {1875-7855}, abstract = {It has recently become possible to start exploring how the genotype translates into human brain morphology and behavior by combining detailed genomic and phenotypic data from thousands of present-day people with archaic genomes of extinct humans, and gene expression data. As a starting point into this emerging interdisciplinary domain, we highlight current debates about which aspects of the modern human brain are unique. We review recent developments from (1) comparative primate neuroscience-a fast-growing field offering an invaluable framework for understanding general mechanisms and the evolution of human-specific traits. (2) paleoanthropology-based on evidence from endocranial imprints in fossil skulls, we trace the evolution from the ape-like brain phenotype of early hominins more than 3 million years ago to the unusual globular brain shape of present-day people. (3) Genomics of present-day and extinct humans. The morphological and genetic differences between modern humans and our closest extinct cousins, the Neandertals, offer important clues about the genetic underpinnings of brain morphology and behavior. The functional consequences of these genetic differences can be tested in animal models, and brain organoids.}, }
@article {pmid36833167, year = {2023}, author = {González-Álvarez, R and Rodríguez-Sánchez, IP and Barrera-Saldaña, HA}, title = {Gene Content and Coding Diversity of the Growth Hormone Loci of Apes.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/genes14020241}, pmid = {36833167}, issn = {2073-4425}, abstract = {The growth hormone (GH) locus has experienced a dramatic evolution in primates, becoming multigenic and diverse in anthropoids. Despite sequence information from a vast number of primate species, it has remained unclear how the multigene family was favored. We compared the structure and composition of apes' GH loci as a prerequisite to understanding their origin and possible evolutionary role. These thorough analyses of the GH loci of the chimpanzee, gorilla, and orangutan were done by resorting to previously sequenced bacterial artificial chromosomes (BACs) harboring them, as well as to their respective genome projects data available in GenBank. The GH loci of modern man, Neanderthal, gibbon, and wild boar were retrieved from GenBank. Coding regions, regulatory elements, and repetitive sequences were identified and compared among species. The GH loci of all the analyzed species are flanked by the genes CD79B (5') and ICAM-1 (3'). In man, Neanderthal, and chimpanzee, the loci were integrated by five almost indistinguishable genes; however, in the former two, they rendered three different hormones, and in the latter, four different proteins were derived. Gorilla exhibited six genes, gibbon seven, and orangutan four. The sequences of the proximal promoters, enhancers, P-elements, and a locus control region (LCR) were highly conserved. The locus evolution might have implicated duplications of the ancestral pituitary gene (GH-N) and subsequent diversification of the copies, leading to the placental single GH-V gene and the multiple CSH genes.}, }
@article {pmid36825485, year = {2023}, author = {Conde-Valverde, M and Martínez, I and Quam, R and Arsuaga, JL}, title = {The ear of the Sima de los Huesos hominins (Atapuerca, Spain).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.25181}, pmid = {36825485}, issn = {1932-8494}, abstract = {Previous studies on the morphology of the inner ear (semicircular canals and cochlea) in the Sima de los Huesos hominin sample have provided important results on the evolution of these structures in the Neandertal lineage. Similarly, studies of the anatomy of the external and middle ear cavities of the Sima de los Huesos hominins have also provided important data on the auditory capacities of this European Middle Pleistocene population. The present contribution provides unpublished data on three new middle ear variables from the Sima de los Huesos fossils and compares these data with values from samples of Pan troglodytes, Homo neanderthalensis and Homo sapiens. The results of this analysis are combined with those obtained in previous studies to characterize the anatomy of the outer, middle and inner ear in the Sima de los Huesos fossils, as well as to establish the order of appearance of the features that characterize Neandertal ears. As in other cranial structures, the ear region in the Sima de los Huesos show a mosaic evolutionary pattern that includes primitive traits, others shared exclusively with Neandertals, and others that are specific to the Sima de los Huesos hominins. Neandertals and Sima de los Huesos hominins share two exclusive features of the middle ear that are among the first characteristics of the Neandertal lineage: a long tympanic cavity and a large entrance and exit of the mastoid antrum. Along with these traits, the Sima de los Huesos hominins present two specialized features: large volumes of the tympanic cavity and the mastoid antrum. Finally, the middle ear of the Neandertals is characterized by the presence of small angles between the tympanic axis and the plane of the oval window.}, }
@article {pmid36823244, year = {2023}, author = {Wang, PY and Yang, Y and Shi, XQ and Chen, Y and Liu, SD and Wang, HY and Peng, T and Shi, Q and Zhang, W and Sun, C}, title = {Distilling functional variations for human UGT2B4 upstream region based on selection signals and implications for phenotypes of Neanderthal and Denisovan.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3134}, pmid = {36823244}, issn = {2045-2322}, abstract = {Our previous work identified one region upstream human UGT2B4 (UDP glucuronosyltransferase family 2 member B4) which is associated with breast cancer and under balancing selection. However, the distribution, functional variation and molecular mechanism underlying breast cancer and balancing selection remain unclear. In current study, the two haplotypes with deep divergence are described by analyzing 1000 genomes project data and observed to be with high frequencies in all human populations. Through population genetics analysis and genome annotation, the potential functional region is identified and verified by reporter gene assay. Further mutagenesis indicates that the functional mutations are rs66862535 and rs68096061. Both SNPs can alter the interaction efficiency of transcription factor POU2F1 (POU class 2 homeobox 1). Through chromosome conformation capture, it is identified that the enhancer containing these two SNPs can interact with UGT2B4 promoter. Expression quantitative trait loci analysis indicates that UGT2B4 expression is dependent on the genotype of this locus. The common haplotype in human is lost in four genomes of archaic hominins, which suggests that Neanderthal and Denisovan should present relatively lower UGT2B4 expression and further higher steroid hormone level. This study provides new insight into the contribution of ancient population structure to human phenotypes.}, }
@article {pmid36821540, year = {2023}, author = {Ghasidian, E and Kafash, A and Kehl, M and Yousefi, M and Heydari-Guran, S}, title = {Modelling Neanderthals' dispersal routes from Caucasus towards east.}, journal = {PloS one}, volume = {18}, number = {2}, pages = {e0281978}, doi = {10.1371/journal.pone.0281978}, pmid = {36821540}, issn = {1932-6203}, abstract = {The study of the cultural materials associated with the Neanderthal physical remains from the sites in the Caucasus, Central Asia and Siberian Altai and adjacent areas documents two distinct techno-complexes of Micoquian and Mousterian. These findings potentially outline two dispersal routes for the Neanderthals out of Europe. Using data on topography and Palaeoclimate, we generated computer-based least-cost-path modelling for the Neanderthal dispersal routes from Caucasus towards the east. In this regard, two dispersal routes have been identified: A northern route from Greater Caucasus associated with Micoquian techno-complex towards Siberian Altai and a southern route from Lesser Caucasus associated with Mousterian towards Siberian Altai via the Southern Caspian Corridor. Based on archaeological, bio- and physio-geographical data, our model hypothesises that during climatic deterioration phases (e.g. MIS 4) the connection between Greater and Lesser Caucasus was limited. This issue perhaps resulted in the separate development and spread of two cultural groups of Micoquian and Mousterian with an input from two different population sources of Neanderthal influxes: eastern and southern Europe refugia for these two northern and southern dispersal routes respectively. Of these two, we focus on the southern dispersal route, for it comprises a 'rapid dispersal route' towards east. The significant location of the Southern Caspian corridor between high mountains of Alborz and the Caspian Sea, provided a special biogeographical zone and a refugium. This exceptional physio-geographic condition brings forward the Southern Caspian corridor as a potential place of admixture of different hominin species including Neanderthals and homo sapiens.}, }
@article {pmid36806751, year = {2023}, author = {Cazenave, M and Radovčić, D}, title = {The Neanderthal patellae from Krapina (Croatia): A comparative investigation of their endostructural conformation and distinctive features compared to the extant human condition.}, journal = {American journal of biological anthropology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ajpa.24709}, pmid = {36806751}, issn = {2692-7691}, abstract = {OBJECTIVES: The Neanderthal patella differs from that of extant humans by being thicker anteroposteriorly and by having more symmetric medial and lateral articular facets. However, it is still unclear to what extent these differences affect knee kinesiology. We aim at assessing the endostructural conformation of Neanderthal patellae to reveal functionally related mechanical information comparatively to the extant human condition. In principle, we expect that the Neanderthal patella (i) shows a higher amount of cortical bone and (ii) a trabecular network organization distinct from the extant human condition.<br><br>MATERIALS AND METHODS: By using micro-focus X-ray tomography, we characterized the endostructure of six adult patellae from the OIS 5e Neanderthal site of Krapina, Croatia, the largest assemblage of human fossil patellae assessed so far, and compared their pattern to the configuration displayed by a sample of 22 recent humans.<br><br>RESULTS AND DISCUSSION: The first expectation is rejected, indicating that the patellar bone might have not followed the trend of generalized gracilization of the human postcranial skeleton occurred through the Upper Pleistocene. The second prediction is at least partially supported. In Krapina the trabecular network differs from the comparative sample by showing a higher medial density and by lacking a proximal reinforcement. Such conformation indicates similar load patterns exerted in Neanderthals and extant humans by the vastus lateralis, but not by the vastus medialis, with implications on the mediolateral stabilization of the knee joint. However, the patterns of structural variation of the patellar network remain to be assessed in other Neanderthal samples.}, }
@article {pmid36796364, year = {2023}, author = {Corcoran, M and Chernyshev, M and Mandolesi, M and Narang, S and Kaduk, M and Ye, K and Sundling, C and Färnert, A and Kreslavsky, T and Bernhardsson, C and Larena, M and Jakobsson, M and Karlsson Hedestam, GB}, title = {Archaic humans have contributed to large-scale variation in modern human T cell receptor genes.}, journal = {Immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.immuni.2023.01.026}, pmid = {36796364}, issn = {1097-4180}, abstract = {Human T cell receptors (TCRs) are critical for mediating immune responses to pathogens and tumors and regulating self-antigen recognition. Yet, variations in the genes encoding TCRs remain insufficiently defined. Detailed analysis of expressed TCR alpha, beta, gamma, and delta genes in 45 donors from four human populations-African, East Asian, South Asian, and European-revealed 175 additional TCR variable and junctional alleles. Most of these contained coding changes and were present at widely differing frequencies in the populations, a finding confirmed using DNA samples from the 1000 Genomes Project. Importantly, we identified three Neanderthal-derived, introgressed TCR regions including a highly divergent TRGV4 variant, which mediated altered butyrophilin-like molecule 3 (BTNL3) ligand reactivity and was frequent in all modern Eurasian population groups. Our results demonstrate remarkable variation in TCR genes in both individuals and populations, providing a strong incentive for including allelic variation in studies of TCR function in human biology.}, }
@article {pmid36791053, year = {2023}, author = {Talamo, S and Kromer, B and Richards, MP and Wacker, L}, title = {Back to the future: The advantage of studying key events in human evolution using a new high resolution radiocarbon method.}, journal = {PloS one}, volume = {18}, number = {2}, pages = {e0280598}, doi = {10.1371/journal.pone.0280598}, pmid = {36791053}, issn = {1932-6203}, abstract = {Radiocarbon dating is the most widely applied dating method in archaeology, especially in human evolution studies, where it is used to determine the chronology of key events, such as the replacement of Neanderthals by modern humans in Europe. However, the method does not always provide precise and accurate enough ages to understand the important processes of human evolution. Here we review the newest method developments in radiocarbon dating ('Radiocarbon 3.0'), which can lead us to much better chronologies and understanding of the major events in recent human evolution. As an example, we apply these new methods to discuss the dating of the important Palaeolithic site of Bacho Kiro (Bulgaria).}, }
@article {pmid36790758, year = {2022}, author = {Oxilia, G and Bortolini, E and Marciani, G and Menghi Sartorio, JC and Vazzana, A and Bettuzzi, M and Panetta, D and Arrighi, S and Badino, F and Figus, C and Lugli, F and Romandini, M and Silvestrini, S and Sorrentino, R and Moroni, A and Donadio, C and Morigi, MP and Slon, V and Piperno, M and Talamo, S and Collina, C and Benazzi, S}, title = {Direct evidence that late Neanderthal occupation precedes a technological shift in southwestern Italy.}, journal = {American journal of biological anthropology}, volume = {179}, number = {1}, pages = {18-30}, doi = {10.1002/ajpa.24593}, pmid = {36790758}, issn = {2692-7691}, abstract = {OBJECTIVES: During the middle-to-upper Paleolithic transition (50,000 and 40,000 years ago), interaction between Neanderthals and Homo sapiens varied across Europe. In southern Italy, the association between Homo sapiens fossils and non-Mousterian material culture, as well as the mode and tempo of Neanderthal demise, are still vividly debated. In this research, we focus on the study of two human teeth by using 3D geometric morphometric approaches for a reliable taxonomical attribution as well as obtaining new radiometric dates on the archeological sequence.<br><br>MATERIAL AND METHODS: This work presents two lower deciduous molars uncovered at Roccia San Sebastiano (Mondragone-Caserta, Italy), stratigraphically associated with Mousterian (RSS1) and Uluzzian (RSS2) artifacts. To obtain a probabilistic attribution of the two RSS teeth to each reference taxa group composed of Neanderthals and Homo sapiens, we performed and compared the performance of three supervised learning algorithms (flexible discriminant analysis, multiadaptive regression splines, and random forest) on both crown and cervical outlines obtained by virtual morphometric methods.<br><br>RESULTS: We show that RSS1, whose Mousterian context appears more recent than 44,800-44,230&#x2009;cal BP, can be attributed to a Neanderthal, while RSS2, found in an Uluzzian context that we dated to 42,640-42,380&#x2009;cal BP, is attributed to Homo sapiens.<br><br>DISCUSSION: This site yields the most recent direct evidence for a Neanderthal presence in southern Italy and confirms a later shift to upper Paleolithic technology in southwestern Italy compared to the earliest Uluzzian evidence at Grotta del Cavallo (Puglia, Italy).}, }
@article {pmid36778254, year = {2023}, author = {Velazquez-Arcelay, K and Colbran, LL and McArthur, E and Brand, C and Siemann, J and McMahon, D and Capra, JA}, title = {Neanderthal Introgression Shaped Human Circadian Traits.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.02.03.527061}, pmid = {36778254}, abstract = {INTRODUCTION: When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultra-violet radiation and an increased variation in seasonal dynamics. However, whether these groups differed substantially in circadian biology, and whether archaic introgression adaptively contributed to human chronotypes remains unknown.<br><br>RESULTS: Here we traced the evolution of chronotype based on genomes from archaic hominin and present-day humans. First, we inferred differences in circadian gene sequences, splicing, and regulation between archaic hominins and modern humans. We identified 28 circadian genes containing variants likely to alter splicing in archaics (e.g., CLOCK, PER2, RORB, RORC), and 16 circadian genes likely divergently regulated between present-day humans and archaic hominins, including RORA . These differences suggest the potential for introgression to modify circadian gene expression. Testing this hypothesis, we found that introgressed variants are enriched among eQTLs for circadian genes. Supporting the functional relevance of these regulatory effects, we found that many introgressed alleles have strong associations with chronotype. Strikingly, the strongest introgressed effects on chronotype increase morningness, which is consistent with adaptations to high latitude in other species. Finally, we identified 26 circadian loci with evidence of adaptive introgression, including PER2 and MYBBP1A .<br><br>CONCLUSIONS: These findings identify differences in circadian gene regulation between modern humans and archaic hominins and support the contribution of introgression via coordinated effects on variation in human chronotype.<br><br>SIGNIFICANCE STATEMENT: Interbreeding between modern humans and Neanderthals created the potential for adaptive introgression as humans moved into new environments that had been populated by Neanderthals for hundreds of thousands of years. Here we discover substantial lineage-specific genetic differences in circadian genes and their regulatory elements between humans and Neanderthals. We then show that introgressed archaic alleles are enriched for effects on circadian gene regulation and consistently increase propensity for morningness in modern Europeans. These results substantially expand our understanding of how the genomes of humans and our closest relatives responded to living in environments with different light/dark cycles, and they demonstrate a coordinated contribution of archaic admixture to modern human chronotype in a direction that is consistent with adaptation to higher latitudes.}, }
@article {pmid36776693, year = {2023}, author = {Hagymási, K}, title = {The Nobel prize in physiology and medicine - 2022.}, journal = {Structural chemistry}, volume = {}, number = {}, pages = {1-4}, pmid = {36776693}, issn = {1040-0400}, abstract = {The Nobel Assembly at Karolinska Institutet awarded the 2022 Nobel Prize in Physiology or Medicine to a Swedish geneticist, Svante Pääbo, for his discoveries concerning the genomes of extinct hominins and human evolution, for the sequencing of the genome of the Neanderthal, the discovery of a previously unknown hominin, Denisova, and the establishment of a new scientific discipline, paleogenomics.}, }
@article {pmid36763080, year = {2023}, author = {Jagoda, E and Marnetto, D and Senevirathne, G and Gonzalez, V and Baid, K and Montinaro, F and Richard, D and Falzarano, D and LeBlanc, EV and Colpitts, CC and Banerjee, A and Pagani, L and Capellini, TD}, title = {Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, doi = {10.7554/eLife.71235}, pmid = {36763080}, issn = {2050-084X}, abstract = {Individuals infected with the SARS-CoV-2 virus present with a wide variety of symptoms ranging from asymptomatic to severe and even lethal outcomes. Past research has revealed a genetic haplotype on chromosome 3 that entered the human population via introgression from Neanderthals as the strongest genetic risk factor for the severe response to COVID-19. However, the specific variants along this introgressed haplotype that contribute to this risk and the biological mechanisms that are involved remain unclear. Here, we assess the variants present on the risk haplotype for their likelihood of driving the genetic predisposition to severe COVID-19 outcomes. We do this by first exploring their impact on the regulation of genes involved in COVID-19 infection using a variety of population genetics and functional genomics tools. We then perform a locus-specific massively parallel reporter assay to individually assess the regulatory potential of each allele on the haplotype in a multipotent immune-related cell line. We ultimately reduce the set of over 600 linked genetic variants to identify four introgressed alleles that are strong functional candidates for driving the association between this locus and severe COVID-19. Using reporter assays in the presence/absence of SARS-CoV-2, we find evidence that these variants respond to viral infection. These variants likely drive the locus' impact on severity by modulating the regulation of two critical chemokine receptor genes: CCR1 and CCR5. These alleles are ideal targets for future functional investigations into the interaction between host genomics and COVID-19 outcomes.}, }
@article {pmid36749731, year = {2023}, author = {Kozowyk, PRB}, title = {Archaeological Podocarpus tar supports the cognitive complexity of Neanderthals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {7}, pages = {e2221676120}, doi = {10.1073/pnas.2221676120}, pmid = {36749731}, issn = {1091-6490}, }
@article {pmid36741450, year = {2022}, author = {Sironi, M and Cagliani, R and Biasin, M and Lo Caputo, S and Saulle, I and Forni, D and Real, LM and Pineda, JA and Exposito, A and Saez, ME and Sinangil, F and Forthal, D and Caruz, A and Clerici, M}, title = {No association of a risk variant for severe COVID-19 with HIV protection in three cohorts of highly exposed individuals.}, journal = {PNAS nexus}, volume = {1}, number = {3}, pages = {pgac138}, pmid = {36741450}, issn = {2752-6542}, abstract = {An extended haplotype on chromosome 3 is the major genetic risk factor for severe COVID-19. The risk haplotype, which was inherited from Neanderthals, decreases the expression of several cytokine receptors, including CCR5. Recently, a study based on three general population cohorts indicated that the minor allele of one of the variants in the haplotype (rs17713054) protects against HIV infection. We thus expected this allele to be over-represented in highly exposed individuals who remain uninfected (exposed seronegative individuals, ESN). To perform a meta-analysis, we genotyped rs17713054 in three ESN cohorts of European ancestry exposed to HIV through different routes. No evidence of association was detected in the single cohorts. The meta-analysis also failed to detect any effect of the variant on protection from HIV-1. The same results were obtained in a Cox-regression analysis for the time to seroconversion. An in-vitro infection assay did not detect differences in viral replication as a function of rs17713054 genotype status. We conclude that the rs17713054 minor allele is not associated with the ESN phenotype and does not modulate HIV infection in vitro.}, }
@article {pmid36730401, year = {2023}, author = {Curry, A}, title = {Neanderthals lived in groups big enough to eat giant elephants.}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6631}, pages = {428}, doi = {10.1126/science.adg9448}, pmid = {36730401}, issn = {1095-9203}, abstract = {Meat from the butchered beasts would have fed hundreds.}, }
@article {pmid36724231, year = {2023}, author = {Gaudzinski-Windheuser, S and Kindler, L and MacDonald, K and Roebroeks, W}, title = {Hunting and processing of straight-tusked elephants 125.000 years ago: Implications for Neanderthal behavior.}, journal = {Science advances}, volume = {9}, number = {5}, pages = {eadd8186}, doi = {10.1126/sciadv.add8186}, pmid = {36724231}, issn = {2375-2548}, abstract = {Straight-tusked elephants (Palaeoloxodon antiquus) were the largest terrestrial mammals of the Pleistocene, present in Eurasian landscapes between 800,000 and 100,000 years ago. The occasional co-occurrence of their skeletal remains with stone tools has generated rich speculation about the nature of interactions between these elephants and Pleistocene humans: Did hominins scavenge on elephants that died a natural death or maybe even hunt some individuals? Our archaeozoological study of the largest P. antiquus assemblage known, excavated from 125,000-year-old lake deposits in Germany, shows that hunting of elephants weighing up to 13 metric tons was part of the cultural repertoire of Last Interglacial Neanderthals there, over >2000 years, many dozens of generations. The intensity and nutritional yields of these well-documented butchering activities, combined with previously reported data from this Neumark-Nord site complex, suggest that Neanderthals were less mobile and operated within social units substantially larger than commonly envisaged.}, }
@article {pmid36719913, year = {2023}, author = {Ben-Dor, M and Barkai, R}, title = {A limited protein high-fat diet may explain the low δ[66]Zn conundrum in the Neandertal from Gabasa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {6}, pages = {e2218081120}, doi = {10.1073/pnas.2218081120}, pmid = {36719913}, issn = {1091-6490}, }
@article {pmid36712807, year = {2022}, author = {Williams, SA and Zeng, I and Paton, GJ and Yelverton, C and Dunham, C and Ostrofsky, KR and Shukman, S and Avilez, MV and Eyre, J and Loewen, T and Prang, TC and Meyer, MR}, title = {Inferring lumbar lordosis in Neandertals and other hominins.}, journal = {PNAS nexus}, volume = {1}, number = {1}, pages = {pgab005}, pmid = {36712807}, issn = {2752-6542}, abstract = {Lumbar lordosis is a key adaptation to bipedal locomotion in the human lineage. Dorsoventral spinal curvatures enable the body's center of mass to be positioned above the hip, knee, and ankle joints, and minimize the muscular effort required for postural control and locomotion. Previous studies have suggested that Neandertals had less lordotic (ventrally convex) lumbar columns than modern humans, which contributed to historical perceptions of postural and locomotor differences between the two groups. Quantifying lower back curvature in extinct hominins is entirely reliant upon bony correlates of overall lordosis, since the latter is significantly influenced by soft tissue structures (e.g. intervertebral discs). Here, we investigate sexual dimorphism, ancestry, and lifestyle effects on lumbar vertebral body wedging and inferior articular facet angulation, two features previously shown to be significantly correlated with overall lordosis in living individuals, in a large sample of modern humans and Neandertals. Our results demonstrate significant differences between postindustrial cadaveric remains and archaeological samples of people that lived preindustrial lifestyles. We suggest these differences are related to activity and other aspects of lifestyle rather than innate population (ancestry) differences. Neandertal bony correlates of lumbar lordosis are significantly different from all human samples except preindustrial males. Therefore, although Neandertals demonstrate more bony kyphotic wedging than most modern humans, we cast doubt on proposed locomotor and postural differences between the two lineages based on inferred lumbar lordosis (or lack thereof), and we recommend future research compare fossils to modern humans from varied populations and not just recent, postindustrial samples.}, }
@article {pmid36711923, year = {2023}, author = {Flegontov, P and Işıldak, U and Maier, R and Yüncü, E and Changmai, P and Reich, D}, title = {Modeling of African population history using f -statistics can be highly biased and is not addressed by previously suggested SNP ascertainment schemes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.01.22.525077}, pmid = {36711923}, abstract = {f -statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. These statistics can provide strong evidence for either admixture or cladality, which can be robust to substantial rates of errors or missing data. f -statistics are guaranteed to be unbiased under "SNP ascertainment" (analyzing non-randomly chosen subsets of single nucleotide polymorphisms) only if it relies on a population that is an outgroup for all groups analyzed. However, ascertainment on a true outgroup that is not co-analyzed with other populations is often impractical and uncommon in the literature. In this study focused on practical rather than theoretical aspects of SNP ascertainment, we show that many non-outgroup ascertainment schemes lead to false rejection of true demographic histories, as well as to failure to reject incorrect models. But the bias introduced by common ascertainments such as the 1240K panel is mostly limited to situations when more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans) or non-human outgroups are co-modelled, for example, f 4 -statistics involving one non-African group, two African groups, and one archaic group. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, cannot fix all these problems since for some classes of f -statistics it is not a clean outgroup ascertainment, and in other cases it demonstrates relatively low power to reject incorrect demographic models since it provides a relatively small number of variants common in anatomically modern humans. And due to the paucity of high-coverage archaic genomes, archaic individuals used for ascertainment often act as sole representatives of the respective groups in an analysis, and we show that this approach is highly problematic. By carrying out large numbers of simulations of diverse demographic histories, we find that bias in inferences based on f -statistics introduced by non-outgroup ascertainment can be minimized if the derived allele frequency spectrum in the population used for ascertainment approaches the spectrum that existed at the root of all groups being co-analyzed. Ascertaining on sites with variants common in a diverse group of African individuals provides a good approximation to such a set of SNPs, addressing the great majority of biases and also retaining high statistical power for studying population history. Such a "pan-African" ascertainment, although not completely problem-free, allows unbiased exploration of demographic models for the widest set of archaic and modern human populations, as compared to the other ascertainment schemes we explored.}, }
@article {pmid36711776, year = {2023}, author = {Witt, KE and Funk, A and Fang, LL and Huerta-Sanchez, E}, title = {The impact of modern admixture on archaic human ancestry in human populations.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.01.16.524232}, pmid = {36711776}, abstract = {Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, as well as introgression between humans and archaic humans, Neanderthals and Denisovans. One example are genomes from populations in the Americas, as these are often mosaics of different ancestries due to recent admixture events as part of European colonization. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual’s archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight enrichment of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.}, }
@article {pmid36707713, year = {2023}, author = {}, title = {Neanderthals stashed dozens of animal skulls in a cave - but why?.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {36707713}, issn = {1476-4687}, }
@article {pmid36593352, year = {2023}, author = {Montag, A}, title = {[The history of skin color is the history of mankind!].}, journal = {Dermatologie (Heidelberg, Germany)}, volume = {74}, number = {2}, pages = {75-79}, pmid = {36593352}, issn = {2731-7013}, mesh = {Animals ; Humans ; *Hominidae/genetics ; Skin Pigmentation/genetics ; *Neanderthals ; Africa, Eastern ; Hair Color/genetics ; }, abstract = {In the early days of mankind, at a time when various other human species populated the earth coexisting with Homo sapiens, the genetic mixing of mankind had already begun. Today, paleogenetics-as a branch of human genetic research-can prove that individuals from the most diverse human species already produced offspring together long before our era. This intermixing was supported from the beginning by massive migratory movements that started in East Africa and led first Homo neanderthalensis and much later also Homo sapiens to as far as Europe-two human species of which we know today that they were lighter-skinned than their ancestors. The adaptation to life in different climatic zones led to development of specific characteristics, which, in addition to physique and physiognomy, also affect specific features of the skin and the integumentary system. The most striking feature among these is the skin color and all associated skin-specific characteristics. These characteristics ensure special protection, but can also be the origin for specific diseases. Any division of Homo sapiens into races has been scientifically refuted. Due to ongoing genetic mixing of mankind, skin color, hair color and all associated characteristics should always be considered individually.}, }
@article {pmid36702939, year = {2023}, author = {Baquedano, E and Arsuaga, JL and Pérez-González, A and Laplana, C and Márquez, B and Huguet, R and Gómez-Soler, S and Villaescusa, L and Galindo-Pellicena, M&#xc1; and Rodríguez, L and García-González, R and Ortega, MC and Martín-Perea, DM and Ortega, AI and Hernández-Vivanco, L and Ruiz-Liso, G and Gómez-Hernanz, J and Alonso-Martín, JI and Abrunhosa, A and Moclán, A and Casado, AI and Vegara-Riquelme, M and Álvarez-Fernández, A and Domínguez-García, &#xc1;C and Álvarez-Lao, DJ and García, N and Sevilla, P and Blain, HA and Ruiz-Zapata, B and Gil-García, MJ and Álvarez-Vena, A and Sanz, T and Quam, R and Higham, T}, title = {A symbolic Neanderthal accumulation of large herbivore crania.}, journal = {Nature human behaviour}, volume = {}, number = {}, pages = {}, pmid = {36702939}, issn = {2397-3374}, abstract = {This work examines the possible behaviour of Neanderthal groups at the Cueva Des-Cubierta (central Spain) via the analysis of the latter's archaeological assemblage. Alongside evidence of Mousterian lithic industry, Level 3 of the cave infill was found to contain an assemblage of mammalian bone remains dominated by the crania of large ungulates, some associated with small hearths. The scarcity of post-cranial elements, teeth, mandibles and maxillae, along with evidence of anthropogenic modification of the crania (cut and percussion marks), indicates that the carcasses of the corresponding animals were initially processed outside the cave, and the crania were later brought inside. A second round of processing then took place, possibly related to the removal of the brain. The continued presence of crania throughout Level 3 indicates that this behaviour was recurrent during this level's formation. This behaviour seems to have no subsistence-related purpose but to be more symbolic in its intent.}, }
@article {pmid36691623, year = {2023}, author = {de March, CA and Matsunami, H and Abe, M and Cobb, M and Hoover, KC}, title = {Genetic and functional odorant receptor variation in the Homo lineage.}, journal = {iScience}, volume = {26}, number = {1}, pages = {105908}, pmid = {36691623}, issn = {2589-0042}, abstract = {Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. Our extinct relatives had highly conserved olfactory receptor sequence, but humans did not. Variations in odorant receptor protein sequence and structure may have produced variation in odor detection and perception. Variants led to minimal changes in specificity but had more influence on functional sensitivity. The few Neanderthal variants disturbed function, whereas Denisovan variants increased sensitivity to sweet and sulfur odors. Geographic adaptations may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. Our survey of olfactory genes and odorant receptors suggests that our genus has a shared repertoire with possible local ecological adaptations.}, }
@article {pmid36681659, year = {2022}, author = {Zhou, Z and M A Swagemakers, S and S Lourens, M and Suratannon, N and J van der Spek, P and A S H Dalm, V and A Dik, W and IJspeert, H and van Hagen, PM}, title = {Did variants in inborn errors of immunity genes contribute to the extinction of Neanderthals?.}, journal = {Asian Pacific journal of allergy and immunology}, volume = {40}, number = {4}, pages = {422-434}, doi = {10.12932/AP-251022-1489}, pmid = {36681659}, issn = {0125-877X}, abstract = {BACKGROUND: Neanderthals were a species of archaic humans that became extinct around 40,000 years ago. Modern humans have inherited 1-6% of Neanderthal DNA as a result of interbreeding. These inherited Neanderthal genes have paradoxical influences, while some can provide protection to viral infections, some others are associated with autoimmune/auto-inflammatory diseases.<br><br>OBJECTIVE: We aim to investigate whether genetic variants with strong detrimental effects on the function of the immune system could have potentially contributed to the extinction of the Neanderthal population.<br><br>METHODS: We used the publically available genome information from an Altai Neanderthal and filtered for potentially damaging variants present in genes associated with inborn errors of immunity (IEI) and checked whether these variants were present in the genomes of the Denisovan, Vindija and Chagyrskaya Neanderthals.<br><br>RESULTS: We identified 24 homozygous variants and 15 heterozygous variants in IEI-related genes in the Altai Neanderthal. Two homozygous variants in the UNC13D gene and one variant in the MOGS gene were present in all archaic genomes. Defects in the UNC13D gene are known to cause a severe and often fatal disease called hemophagocytic lymphohistiocystosis (HLH). One of these variants p.(N943S) has been reported in patients with HLH. Variants in MOGS are associated with glycosylation defects in the immune system affecting the susceptibility for infections.<br><br>CONCLUSIONS: Although the exact functional impact of these three variants needs further elucidation, we speculate that they could have resulted in an increased susceptibility to severe diseases and may have contributed to the extinction of Neanderthals after exposure to specific infections.}, }
@article {pmid36679036, year = {2023}, author = {Nezami, E and Gallego, PP}, title = {History, Phylogeny, Biodiversity, and New Computer-Based Tools for Efficient Micropropagation and Conservation of Pistachio (Pistacia spp.) Germplasm.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/plants12020323}, pmid = {36679036}, issn = {2223-7747}, abstract = {The word "pstk" [pistag], used in the ancient Persian language, is the linguistic root from which the current name "pistachio", used worldwide, derives. The word pistachio is generally used to designate the plants and fruits of a single species: Pistacia vera L. Both the plant and its fruits have been used by mankind for thousands of years, specifically the consumption of its fruits by Neanderthals has been dated to about 300,000 years ago. Native to southern Central Asia (including northern Afghanistan and northeastern Iran), its domestication and cultivation occurred about 3000 years ago in this region, spreading to the rest of the Mediterranean basin during the Middle Ages and finally being exported to America and Australia at the end of the 19th century. The edible pistachio is an excellent source of unsaturated fatty acids, carbohydrates, proteins, dietary fiber, vitamins, minerals and bioactive phenolic compounds that help promote human health through their antioxidant capacity and biological activities. The distribution and genetic diversity of wild and domesticated pistachios have been declining due to increasing population pressure and climatic changes, which have destroyed natural pistachio habitats, and the monoculture of selected cultivars. As a result, the current world pistachio industry relies mainly on a very small number of commercial cultivars and rootstocks. In this review we discuss and summarize the current status of: etymology, origin, domestication, taxonomy and phylogeny by molecular analysis (RAPID, RFLP, AFLP, SSR, ISSR, IRAP, eSSR), main characteristics and world production, germplasm biodiversity, main cultivars and rootstocks, current conservation strategies of both conventional propagation (seeds, cutting, and grafting), and non-conventional propagation methods (cryopreservation, slow growth storage, synthetic seed techniques and micropropagation) and the application of computational tools (Design of Experiments (DoE) and Machine Learning: Artificial Neural Networks, Fuzzy logic and Genetic Algorithms) to design efficient micropropagation protocols for the genus Pistacia.}, }
@article {pmid36656646, year = {2023}, author = {García-González, R and Rodríguez, L and Salazar-Fernández, A and Arsuaga, JL and Carretero, JM}, title = {Updated study of adult and subadult pectoral girdle bones from Sima de los Huesos site (Sierra de Atapuerca, Burgos, Spain). Anatomical and age estimation keys.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.25158}, pmid = {36656646}, issn = {1932-8494}, abstract = {Here we present an updated inventory and study of pectoral girdle remains recovered from the Sima de los Huesos (SH) site. Here, we describe the key morphological traits of adults and, for the first time, subadult specimens. Because morphological traits can change with age, we also discuss some shortcomings related to age estimation in postcranial fossil specimens. Adult clavicles from the SH are long with a low robusticity index and marked curvatures in the superior view. Among these traits, only extreme clavicular length seems to characterize subadult individuals. Neandertals share all these traits. In the case of the scapula, the SH specimens share a relatively long and narrow glenoid fossa with Neandertals. This trait is also present in subadult individuals. Additionally, most specimens from SH, adults, and subadults showed a dorsal axillary sulcus on the scapular lateral border, a trait also present in most adult and subadult Neandertals. These traits in adult and subadult specimens supports substantial genetic control for many of them in both human species.}, }
@article {pmid36652426, year = {2023}, author = {Berlioz, E and Capdepon, E and Discamps, E}, title = {A long-term perspective on Neanderthal environment and subsistence: Insights from the dental microwear texture analysis of hunted ungulates at Combe-Grenal (Dordogne, France).}, journal = {PloS one}, volume = {18}, number = {1}, pages = {e0278395}, doi = {10.1371/journal.pone.0278395}, pmid = {36652426}, issn = {1932-6203}, abstract = {Large bovids and cervids constituted major components of the European Middle Palaeolithic faunas and hence a key resource for Neanderthal populations. In paleoenvironmental reconstructions, red deer (Cervus elaphus) occurrence is classically considered as a tree-cover indicator while Bovinae (Bison priscus and Bos primigenius) and reindeer (Rangifer tarandus) occurrences are typically associated with open landscapes. However, insights into the ecology of extant ungulate populations show a more complex reality. Exploring the diet of past ungulates allows to better comprehend the hunting strategies of Palaeolithic populations and to reconstruct the modifications through time of past landscapes. By reflecting what animals have eaten during the last days or weeks of their life, dental microwear textures of herbivores link a population and its environment. Here we analyzed, via Dental Microwear Texture Analysis (DMTA), the diet of 50 Bos/Bison, 202 R. tarandus and 116 C. elaphus preyed upon by the Neanderthals that occupied Combe-Grenal rock-shelter, one of the most important Mousterian archaeo-sequences in southwestern France considering its long stratigraphy, abundance of faunal remains and the variations perceptible in Palaeolithic material culture. Grazers and mixed-feeders are the most represented dietary categories among Combe-Grenal's guild of herbivores, highlighting the availability, along the sequence, of open landscapes. The absence of clear changes in the use of plant resources by hunted ungulates through time, even though palaeoenvironmental changes were well-documented by previous studies along the sequence, is interpreted as resulting from the hunting of non-randomly selected prey by Neanderthals, preferentially in open environments. Thus, these results provide further insight into the hunting strategies of Neanderthals and modify our perception of potential links between subsistence and material culture. Combe-Grenal hunters "stayed in the open" through millennia, and were not forced to switch to hunting tactics and material technology adapted to close encounters in forested environments.}, }
@article {pmid36651963, year = {2023}, author = {Moreira, F and Arenas, M and Videira, A and Pereira, F}, title = {Evolution of TOP1 and TOP1MT Topoisomerases in Chordata.}, journal = {Journal of molecular evolution}, volume = {}, number = {}, pages = {}, pmid = {36651963}, issn = {1432-1432}, abstract = {Type IB topoisomerases relax the torsional stress associated with DNA metabolism in the nucleus and mitochondria and constitute important molecular targets of anticancer drugs. Vertebrates stand out among eukaryotes by having two Type IB topoisomerases acting specifically in the nucleus (TOP1) and mitochondria (TOP1MT). Despite their major importance, the origin and evolution of these paralogues remain unknown. Here, we examine the molecular evolutionary processes acting on both TOP1 and TOP1MT in Chordata, taking advantage of the increasing number of available genome sequences. We found that both TOP1 and TOP1MT evolved under strong purifying selection, as expected considering their essential biological functions. Critical active sites, including those associated with resistance to anticancer agents, were found particularly conserved. However, TOP1MT presented a higher rate of molecular evolution than TOP1, possibly related with its specialized activity on the mitochondrial genome and a less critical role in cells. We could place the duplication event that originated the TOP1 and TOP1MT paralogues early in the radiation of vertebrates, most likely associated with the first round of vertebrate tetraploidization (1R). Moreover, our data suggest that cyclostomes present a specialized mitochondrial Type IB topoisomerase. Interestingly, we identified two missense mutations replacing amino acids in the Linker region of TOP1MT in Neanderthals, which appears as a rare event when comparing the genome of both species. In conclusion, TOP1 and TOP1MT differ in their rates of evolution, and their evolutionary histories allowed us to better understand the evolution of chordates.}, }
@article {pmid36625544, year = {2023}, author = {Aqil, A and Speidel, L and Pavlidis, P and Gokcumen, O}, title = {Balancing selection on genomic deletion polymorphisms in humans.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, doi = {10.7554/eLife.79111}, pmid = {36625544}, issn = {2050-084X}, abstract = {A key question in biology is why genomic variation persists in a population for extended periods. Recent studies have identified examples of genomic deletions that have remained polymorphic in the human lineage for hundreds of millennia, ostensibly owing to balancing selection. Nevertheless, genome-wide investigation of ancient and possibly adaptive deletions remains imperative. Here, we demonstrate an excess of polymorphisms in present-day humans that predate the modern human-Neanderthal split (ancient polymorphisms), which cannot be explained solely by selectively neutral scenarios. We analyze the adaptive mechanisms that underlie this excess in deletion polymorphisms. Using a previously published measure of balancing selection, we show that this excess of ancient deletions is largely owing to balancing selection. Based on the absence of signatures of overdominance, we conclude that it is a rare mode of balancing selection among ancient deletions. Instead, more complex scenarios involving spatially and temporally variable selective pressures are likely more common mechanisms. Our results suggest that balancing selection resulted in ancient deletions harboring disproportionately more exonic variants with GWAS associations. We further found that ancient deletions are significantly enriched for traits related to metabolism and immunity. As a by-product of our analysis, we show that deletions are, on average, more deleterious than single-nucleotide variants. We can now argue that not only is a vast majority of common variants shared among human populations, but a considerable portion of biologically relevant variants has been segregating among our ancestors for hundreds of thousands, if not millions, of years.}, }
@article {pmid36617238, year = {2023}, author = {Zhang, X and Kim, B and Singh, A and Sankararaman, S and Durvasula, A and Lohmueller, KE}, title = {MaLAdapt reveals novel targets of adaptive introgression from Neanderthals and Denisovans in worldwide human populations.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad001}, pmid = {36617238}, issn = {1537-1719}, abstract = {Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, approaches intersecting outliers are vulnerable to a high false-negative rate as the power of different methods varies, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals to AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present a ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selective sweeps, heterosis from deleterious mutations, and demographic misspecification. Further, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and on a validation of empirical signals through visual inspection of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data, and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.}, }
@article {pmid36604552, year = {2023}, author = {Sansalone, G and Profico, A and Wroe, S and Allen, K and Ledogar, J and Ledogar, S and Mitchell, DR and Mondanaro, A and Melchionna, M and Castiglione, S and Serio, C and Raia, P}, title = {Homo sapiens and Neanderthals share high cerebral cortex integration into adulthood.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {36604552}, issn = {2397-334X}, abstract = {There is controversy around the mechanisms that guided the change in brain shape during the evolution of modern humans. It has long been held that different cortical areas evolved independently from each other to develop their unique functional specializations. However, some recent studies suggest that high integration between different cortical areas could facilitate the emergence of equally extreme, highly specialized brain functions. Here, we analyse the evolution of brain shape in primates using three-dimensional geometric morphometrics of endocasts. We aim to determine, firstly, whether modern humans present unique developmental patterns of covariation between brain cortical areas; and secondly, whether hominins experienced unusually high rates of evolution in brain covariation as compared to other primates. On the basis of analyses including modern humans and other extant great apes at different developmental stages, we first demonstrate that, unlike our closest living relatives, Homo sapiens retain high levels of covariation between cortical areas into adulthood. Among the other great apes, high levels of covariation are only found in immature individuals. Secondly, at the macro-evolutionary level, our analysis of 400 endocasts, representing 148 extant primate species and 6 fossil hominins, shows that strong covariation between different areas of the brain in H. sapiens and Homo neanderthalensis evolved under distinctly higher evolutionary rates than in any other primate, suggesting that natural selection favoured a greatly integrated brain in both species. These results hold when extinct species are excluded and allometric effects are accounted for. Our findings demonstrate that high covariation in the brain may have played a critical role in the evolution of unique cognitive capacities and complex behaviours in both modern humans and Neanderthals.}, }
@article {pmid36594678, year = {2023}, author = {Laudicina, NM and Cartmill, M}, title = {Clavicle length and shoulder breadth in hominoid evolution.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.25144}, pmid = {36594678}, issn = {1932-8494}, abstract = {For a given body mass, hominoids have longer clavicles than typical monkeys, reflecting the lateral reorientation of the hominoid glenoid. Relative length of the clavicle varies among hominoids, with orangutans having longer clavicles than expected for body mass and gorillas and chimpanzees having shorter clavicles than expected. Modern humans conform to the general hominoid distribution, but Neandertals and Upper Paleolithic Homo sapiens have longer clavicles than expected for their size and exhibit marked positive allometry in clavicle length. Relative to clavicle length, adult and newborn humans have broader shoulders (biacromial breadths) than comparable apes, because the reduced elevation of the human shoulder swings the acromion laterally downward away from the head. Since broadened shoulders yield an increased risk of maternal and neonatal injury and/or death from shoulder dystocia during birth, we might expect hominins to manifest trends toward reduction in shoulder breadth and clavicle length. They do not, presumably because of countering selection pressures favoring a long clavicle in the adults. The marked sexual dimorphism seen in patterns of clavicular growth and static adult allometry in humans suggests that those selection pressures have disproportionately affected the males.}, }
@article {pmid36576952, year = {2022}, author = {Peresani, M}, title = {Inspecting human evolution from a cave. Late Neanderthals and early sapiens at Grotta di Fumane: present state and outlook.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {100}, number = {}, pages = {}, doi = {10.4436/JASS.10016}, pmid = {36576952}, issn = {2037-0644}, abstract = {Of the many critical phases of human evolution, one of the most investigated is the transition from the Middle to the Upper Palaeolithic with the pivotal bio-cultural substitution of Neanderthals by Homo sapiens in Western Eurasia. The complexity of this over ten thousands years phase raises from the ensemble of evidence ascribed to the diverse adaptations expressed by Neanderthals and the first representatives of our species. In countless archaeological records Neanderthals left clear traces of a cultural variability dotted with innovations in the technology of stone and bone tools, alongside with manifestations in the range of the symbolic sphere. Together with other aspects of daily life, this evidence contributes shedding light on the cognitive aptitudes of those hominins and reassessing gaps in Pleistocene human diversities. Among archaeological contexts, the cave of Fumane in the Monti Lessini (Veneto Pre-Alps, northeastern Italy) is a key site. It is positioned along the potential trajectory of hominins moving into southern Europe from eastern and southeastern regions and includes a finely layered sedimentary sequence with cultural layers ascribed to the Mousterian, Uluzzian, Aurignacian and Gravettian. The ensemble constitutes one of the most complete, detailed and dated continental stratigraphic series from a segment of the late Pleistocene between 50 and 30 ka cal BP in a cave context of Southern Europe. Assessments based on sedimentological and palaeontological record provide indicators for framing Neanderthals in their respective ecological contexts since the late Middle Pleistocene until their demise during MIS3. On-going research is producing data ascribable to the human ecological relations and the interaction with specific natural resources, thus contributing to shed light on the complexity of Neanderthal behavior. Thanks to the high-resolution archaeological record of the earliest appearances of Homo sapiens, Fumane also provides clues to compare life, subsistence, and cultures between these Pleistocene hominins for comprehensive reasonings on our unicity.}, }
@article {pmid36564491, year = {2022}, author = {Bañuls-Cardona, S and Blasco, R and Rosell, J and Rufà, A and Vallverdú, J and Rivals, F}, title = {New quantitative method for dental wear analysis of small mammals.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22231}, pmid = {36564491}, issn = {2045-2322}, abstract = {The application of dental wear study to murids has always been ruled out because of their omnivorous diet, which does not leave significant wear on the dentition. Nevertheless, in our work we select Apodemus sylvaticus (wood mouse) as the object of study for several reasons: its seasonal diet, its ability to resist the gastric juices of predators, the fact that it has not undergone major morphological changes since its appearance 3 million years ago, and its widespread distribution throughout much of Europe and part of Africa. The importance of this work lies in the modifications we make to the dental wear methodology for its application to murids. These enable us to obtain quantitative data on the entire tooth surface. The sample chosen was a total of 75 lower first molars from two different archaeological sites: Teixoneres cave and Xaragalls cave. The chronology of the samples chosen ranges from Marine Isotope Stages 5-3. The data obtained reveal that the part of the tooth that shows most wear is the distal part (entoconid). Furthermore, the results provide us with relevant information on the types of accumulations of remains in the caves (short vs. long term), as well as on the seasonality of Neanderthal occupations during the Upper Pleistocene (MIS5-3) of the northeastern Iberian Peninsula.}, }
@article {pmid36560850, year = {2022}, author = {Yermakovich, D and Pankratov, V and Võsa, U and Yunusbayev, B and ,  and Dannemann, M}, title = {Long-range regulatory effects of Neandertal DNA in modern humans.}, journal = {Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/genetics/iyac188}, pmid = {36560850}, issn = {1943-2631}, abstract = {The admixture between modern humans and Neandertals has resulted in ∼2% of the genomes of present-day non-Africans being composed of Neandertal DNA. Introgressed Neandertal DNA has been demonstrated to significantly affect the transcriptomic landscape in people today and via this molecular mechanism influence phenotype variation as well. However, little is known about how much of that regulatory impact is mediated through long-range regulatory effects that have been shown to explain ∼20% of expression variation. Here we identified 60 transcription factors (TFs) with their top cis-eQTL SNP in GTEx being of Neandertal ancestry and predicted long-range Neandertal DNA-induced regulatory effects by screening for the predicted target genes of those TFs. We show that the TFs form a significantly connected protein-protein interaction network. Among them are JUN and PRDM5, two brain-expressed TFs that have their predicted target genes enriched in regions devoid of Neandertal DNA. Archaic cis-eQTLs for the 60 TFs include multiple candidates for local adaptation, some of which show significant allele frequency increases over the last ∼10,000 years. A large proportion of the cis-eQTL-associated archaic SNPs have additional associations with various immune traits, schizophrenia, blood cell type composition and anthropometric measures. Finally, we demonstrate that our results are consistent with those of Neandertal-DNA-associated empirical trans-eQTLs. Our results suggest that Neandertal DNA significantly influences regulatory networks, that its regulatory reach goes beyond the 40% of genomic sequence that it still covers in present-day non-Africans and that via the investigated mechanism Neandertal DNA influences the phenotypic variation in people today.}, }
@article {pmid36520391, year = {2023}, author = {Gorgé, O and Bennett, EA and Massilani, D and Daligault, J and Geigl, EM and Grange, T}, title = {Analysis of Ancient Microbial DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {103-131}, pmid = {36520391}, issn = {1940-6029}, abstract = {The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.}, }
@article {pmid36511798, year = {2022}, author = {Stringer, C}, title = {The development of ideas about a recent African origin for Homo sapiens.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {100}, number = {}, pages = {}, doi = {10.4436/JASS.10009}, pmid = {36511798}, issn = {2037-0644}, abstract = {In this contribution I will review the development of ideas about a recent African origin for our species over the last 50 years, starting from the time of my PhD in the early 1970s. I will examine the instructive and quite different interpretations placed on the 1979 discovery of a partial Neanderthal skeleton associated with a Châtelperronian industry at the rock shelter of St-Césaire in France, and then focus on the crucial years from 1987-1989, including the so-called 'Human Revolution' conference of 1987, and my 1988 Science paper with Peter Andrews: 'Genetic and Fossil Evidence for the Origin of Modern Humans'. Following the historical review, I will assess the status of five proposed models for the evolution of derived Homo sapiens: Recent African Origin (RAO); RAO and Hybridisation (RAOH); Assimilation (AM); Multiregional Evolution (MRE); and Braided Stream (BS). I conclude that a recent African origin model with hybridization (RAOH) is the best supported from the fossil and genetic evidence.}, }
@article {pmid36503519, year = {2022}, author = {Taravella Oill, AM and Buetow, KH and Wilson, MA}, title = {The role of Neanderthal introgression in liver cancer.}, journal = {BMC medical genomics}, volume = {15}, number = {1}, pages = {255}, pmid = {36503519}, issn = {1755-8794}, support = {R35GM124827/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Neanderthal introgressed DNA has been linked to different normal and disease traits including immunity and metabolism-two important functions that are altered in liver cancer. However, there is limited understanding of the relationship between Neanderthal introgression and liver cancer risk. The aim of this study was to investigate the relationship between Neanderthal introgression and liver cancer risk.<br><br>METHODS: Using germline and somatic DNA and tumor RNA from liver cancer patients from The Cancer Genome Atlas, along with ancestry-match germline DNA from unaffected individuals from the 1000 Genomes Resource, and allele specific expression data from normal liver tissue from The Genotype-Tissue Expression project we investigated whether Neanderthal introgression impacts cancer etiology. Using a previously generated set of Neanderthal alleles, we identified Neanderthal introgressed haplotypes. We then tested whether somatic mutations are enriched or depleted on Neanderthal introgressed haplotypes compared to modern haplotypes. We also computationally assessed whether somatic mutations have a functional effect or show evidence of regulating expression of Neanderthal haplotypes. Finally, we compared patterns of Neanderthal introgression in liver cancer patients and the general population.<br><br>RESULTS: We find Neanderthal introgressed haplotypes exhibit an excess of somatic mutations compared to modern haplotypes. Variant Effect Predictor analysis revealed that most of the somatic mutations on these Neanderthal introgressed haplotypes are not functional. We did observe expression differences of Neanderthal alleles between tumor and normal for four genes that also showed a pattern of enrichment of somatic mutations on Neanderthal haplotypes. However, gene expression was similar between liver cancer patients with modern ancestry and liver cancer patients with Neanderthal ancestry at these genes. Provocatively, when analyzing all genes, we find evidence of Neanderthal introgression regulating expression in tumor from liver cancer patients in two genes, ARK1C4 and OAS1. Finally, we find that most genes do not show a difference in the proportion of Neanderthal introgression between liver cancer patients and the general population.<br><br>CONCLUSION: Our results suggest that Neanderthal introgression provides opportunity for somatic mutations to accumulate, and that some Neanderthal introgression may impact liver cancer risk.}, }
@article {pmid36493597, year = {2022}, author = {Keeling, BA and Quam, R and Martínez, I and Arsuaga, JL and Maroto, J}, title = {Reassessment of the human mandible from Banyoles (Girona, Spain).}, journal = {Journal of human evolution}, volume = {174}, number = {}, pages = {103291}, doi = {10.1016/j.jhevol.2022.103291}, pmid = {36493597}, issn = {1095-8606}, abstract = {Since the discovery of a human mandible in 1887 near the present-day city of Banyoles, northeastern Spain, researchers have generally emphasized its archaic features, including the lack of chin structures, and suggested affinities with the Neandertals or European Middle Pleistocene (Chibanian) specimens. Uranium-series and electron spin resonance dating suggest the mandible dates to the Late Pleistocene (Tarantian), approximately ca. 45-66 ka. In this study, we reassessed the taxonomic affinities of the Banyoles mandible by comparing it to samples of Middle Pleistocene fossils from Africa and Europe, Neandertals, Early and Upper Paleolithic modern humans, and recent modern humans. We evaluated the frequencies and expressions of morphological features and performed a three-dimensional geometric morphometric analysis on a virtual reconstruction of Banyoles to capture overall mandibular shape. Our results revealed no derived Neandertal morphological features in Banyoles. While a principal component analysis based on Euclidean distances from the first two principal components clearly grouped Banyoles with both fossil and recent Homo sapiens individuals, an analysis of the Procrustes residuals demonstrated that Banyoles did not fit into any of the comparative groups. The lack of Neandertal features in Banyoles is surprising considering its Late Pleistocene age. A consideration of the Middle Pleistocene fossil record in Europe and southwest Asia suggests that Banyoles is unlikely to represent a late-surviving Middle Pleistocene population. The lack of chin structures also complicates an assignment to H. sapiens, although early fossil H. sapiens do show somewhat variable development of the chin structures. Thus, Banyoles represents a non-Neandertal Late Pleistocene European individual and highlights the continuing signal of diversity in the hominin fossil record. The present situation makes Banyoles a prime candidate for ancient DNA or proteomic analyses, which may shed additional light on its taxonomic affinities.}, }
@article {pmid36480515, year = {2022}, author = {Vespasiani, DM and Jacobs, GS and Cook, LE and Brucato, N and Leavesley, M and Kinipi, C and Ricaut, FX and Cox, MP and Gallego Romero, I}, title = {Denisovan introgression has shaped the immune system of present-day Papuans.}, journal = {PLoS genetics}, volume = {18}, number = {12}, pages = {e1010470}, doi = {10.1371/journal.pgen.1010470}, pmid = {36480515}, issn = {1553-7404}, abstract = {Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.}, }
@article {pmid36471017, year = {2022}, author = {Saraiva, LR}, title = {The Neanderthal inside us.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {36471017}, issn = {1471-0064}, }
@article {pmid36467077, year = {2022}, author = {Schäfer, W and Stähler, T and Pinto Espinoza, C and Danquah, W and Knop, JH and Rissiek, B and Haag, F and Koch-Nolte, F}, title = {Origin, distribution, and function of three frequent coding polymorphisms in the gene for the human P2X7 ion channel.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {1033135}, pmid = {36467077}, issn = {1663-9812}, abstract = {P2X7, an ion channel gated by extracellular ATP, is widely expressed on the plasma membrane of immune cells and plays important roles in inflammation and apoptosis. Several single nucleotide polymorphisms have been identified in the human P2RX7 gene. In contrast to other members of the P2X family, non-synonymous polymorphisms in P2X7 are common. Three of these occur at overall frequencies of more than 25% and affect residues in the extracellular "head"-domain of P2X7 (155 Y/H), its "lower body" (270 R/H), and its "tail" in the second transmembrane domain (348 T/A). Comparison of the P2X7 orthologues of human and other great apes indicates that the ancestral allele is Y-R-T (at 155-270-348). Interestingly, each single amino acid variant displays lower ATP-sensitivity than the ancestral allele. The originally published reference sequence of human P2X7, often referred to as "wildtype," differs from the ancestral allele at all three positions, i.e. H-H-A. The 1,000 Genome Project determined the sequences of both alleles of 2,500 human individuals, including roughly 500 persons from each of the five major continental regions. This rich resource shows that the ancestral alleles Y155, R270, and T348 occur in all analyzed human populations, albeit at strikingly different frequencies in various subpopulations (e.g., 25%-59% for Y155, 59%-77% for R270, and 13%-47% for T348). BLAST analyses of ancient human genome sequences uncovered several homozygous carriers of variant P2X7 alleles, possibly reflecting a high degree of inbreeding, e.g., H-R-T for a 50.000 year old Neanderthal, H-R-A for a 24.000 year old Siberian, and Y-R-A for a 7,000 year old mesolithic European. In contrast, most present-day individuals co-express two copies of P2X7 that differ in one or more amino acids at positions 155, 270, and 348. Our results improve the understanding of how P2X7 structure affects its function and suggest the importance of considering P2X7 variants of participants when designing clinical trials targeting P2X7.}, }
@article {pmid36465121, year = {2022}, author = {Ma, X and Xu, S}, title = {Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia.}, journal = {iScience}, volume = {25}, number = {12}, pages = {105614}, pmid = {36465121}, issn = {2589-0042}, abstract = {Thiamine (vitamin B1) is an essential micronutrient. Genes involved in thiamine metabolisms, such as SLC19A2, SLC35F3, and SLC35F4, were assumed to be underlying positive selection in East Asians, but the detailed mechanism remains unknown. Here, we analyzed genome data of 3,823 individuals representing 223 global populations and identified the adaptive haplotypes at thiamine genes. Interestingly, the putative adaptive haplotype at SLC35F4 was of Neanderthal ancestry, while that at SLC35F3 was also likely of archaic origins. Leveraging new methods and available ancient DNA data, we further demonstrated that the beneficial haplotypes reached a high frequency at least 10,000 years ago and are maintained persistently in present-day East Asians. We argue that pathogens, rather than agriculture developed ∼10,000 years ago in East Asia, were likely the initial driving force of the putative positive selection. Notably, the first American people did not carry the putative adaptive haplotype at SLC35F4.}, }
@article {pmid36455404, year = {2022}, author = {Velez, AD and Quam, R and Conde-Valverde, M and Martínez, I and Lorenzo, C and Arsuaga, JL}, title = {Geometric morphometric analysis of the bony labyrinth of the Sima de los Huesos hominins.}, journal = {Journal of human evolution}, volume = {174}, number = {}, pages = {103280}, doi = {10.1016/j.jhevol.2022.103280}, pmid = {36455404}, issn = {1095-8606}, abstract = {The bony labyrinth contains phylogenetic information that can be used to determine interspecific differences between fossil hominins. The present study conducted a comparative 3D geometric morphometric analysis on the bony labyrinth of the Middle Pleistocene Sima de los Huesos (SH) hominins. The findings of this study corroborate previous multivariate analyses of the SH hominin bony labyrinth. The analysis of the semicircular canals revealed the SH hominin canal morphologies appear closer to those of the Neandertals than to those of Homo sapiens. This is attributable to a Neandertal-like ovoid anterior canal, and mediolaterally expanded, circular posterior canal. However, the SH hominins lack the increased torsion in the anterior canal and the inferior orientation of the lateral canal seen in Neandertals. The results of the cochlear analysis indicated that, although there is some overlap, there are notable differences between the SH hominins and the Neandertals. In particular, the SH hominin cochlea appears more constricted than in Neandertals in the first and second turns. A principal component analysis of the full bony labyrinth separated most SH hominins from the Neandertals, which largely clustered with modern humans. A covariance ratio analysis found a significant degree of modularity within the bony labyrinth of all three groups, with the SH hominins and Neandertals displaying the highest modularity. This modular signal in the bony labyrinth may be attributable to different selective pressures related to locomotion and audition. Overall, the results of this study confirm previous suggestions that the semicircular canals in the SH hominins are somewhat derived toward Neandertals, while their cochlea is largely primitive within the genus Homo.}, }
@article {pmid36455403, year = {2022}, author = {Britton, K and Jimenez, EL and Le Corre, M and Pederzani, S and Daujeard, C and Jaouen, K and Vettese, D and Tütken, T and Hublin, JJ and Moncel, MH}, title = {Multi-isotope zooarchaeological investigations at Abri du Maras: The paleoecological and paleoenvironmental context of Neanderthal subsistence strategies in the Rhône Valley during MIS 3.}, journal = {Journal of human evolution}, volume = {174}, number = {}, pages = {103292}, doi = {10.1016/j.jhevol.2022.103292}, pmid = {36455403}, issn = {1095-8606}, abstract = {The exploitation of mid- and large-sized herbivores (ungulates) was central to hominin subsistence across Late Pleistocene Europe. Reconstructing the paleoecology of prey-taxa is key to better understanding procurement strategies, decisions and behaviors, and the isotope analysis of faunal bones and teeth found at archaeological sites represent a powerful means of accessing information about past faunal behaviors. These isotope zooarchaeological approaches also have a near-unique ability to reveal environmental conditions contemporary to the human activities that produced these remains. Here, we present the results of a multi-isotope, multitissue study of ungulate remains from the Middle Paleolithic site of Abri du Maras, southern France, providing new insights into the living landscapes of the Rhône Valley during MIS 3 (level 4.2 = 55 ± 2 to 42 ± 3 ka; level 4.1 = 46 ± 3 to 40 ± 3 ka). Isotope data (carbon, nitrogen) reveal the dietary niches of different ungulate taxa, including the now-extinct giant deer (Megaloceros). Oxygen isotope data are consistent with a mild seasonal climate during level 4.2, where horse (Equus), bison (Bison), and red deer (Cervus elaphus) were exploited year-round. Strontium and sulfur isotope analyses provide new evidence for behavioral plasticity in Late Pleistocene European reindeer (Rangifer) between level 4.2 and level 4.1, indicating a change from the migratory to the sedentary ecotype. In level 4.1, the strong seasonal nature of reindeer exploitation, combined with their nonmigratory behavior, is consistent with a seasonally restricted use of the site by Neanderthals at that time or the preferential hunting of reindeer when in peak physical condition during the autumn.}, }
@article {pmid36423581, year = {2022}, author = {Mangan, RJ and Alsina, FC and Mosti, F and Sotelo-Fonseca, JE and Snellings, DA and Au, EH and Carvalho, J and Sathyan, L and Johnson, GD and Reddy, TE and Silver, DL and Lowe, CB}, title = {Adaptive sequence divergence forged new neurodevelopmental enhancers in humans.}, journal = {Cell}, volume = {185}, number = {24}, pages = {4587-4603.e23}, doi = {10.1016/j.cell.2022.10.016}, pmid = {36423581}, issn = {1097-4172}, mesh = {Animals ; Humans ; *Hominidae/genetics ; Regulatory Sequences, Nucleic Acid ; *Neanderthals/genetics ; Genome, Human ; Genomics ; }, abstract = {Searches for the genetic underpinnings of uniquely human traits have focused on human-specific divergence in conserved genomic regions, which reflects adaptive modifications of existing functional elements. However, the study of conserved regions excludes functional elements that descended from previously neutral regions. Here, we demonstrate that the fastest-evolved regions of the human genome, which we term "human ancestor quickly evolved regions" (HAQERs), rapidly diverged in an episodic burst of directional positive selection prior to the human-Neanderthal split, before transitioning to constraint within hominins. HAQERs are enriched for bivalent chromatin states, particularly in gastrointestinal and neurodevelopmental tissues, and genetic variants linked to neurodevelopmental disease. We developed a multiplex, single-cell in vivo enhancer assay to discover that rapid sequence divergence in HAQERs generated hominin-unique enhancers in the developing cerebral cortex. We propose that a lack of pleiotropic constraints and elevated mutation rates poised HAQERs for rapid adaptation and subsequent susceptibility to disease.}, }
@article {pmid36418334, year = {2022}, author = {Deschamps, M and Martín-Lerma, I and Linares-Matás, G and Zilhão, J}, title = {Organization of residential space, site function variability, and seasonality of activities among MIS 5 Iberian Neandertals.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20221}, pmid = {36418334}, issn = {2045-2322}, mesh = {Animals ; *Neanderthals ; Archaeology ; Climate ; Seasons ; Anthropology, Cultural ; }, abstract = {Whether ethnoarcheological models of hunter-gatherer mobility, landscape use, and structuration of the inhabited space are relevant to the archeology of Neandertals and the Middle Paleolithic remains controversial. The thin lenses of hearth-associated stone tools and faunal remains excavated in sub-complex AS5 of Cueva Antón (Murcia, Spain) significantly advance these debates. Dated to 77.8-85.1 ka, these living floors are interstratified in river-accumulated sands and were buried shortly after abandonment by low-energy inundation events, with minimal disturbance and negligible palimpsest formation. Stone tools were made and ergonomically modified to fit tasks; their spatial distributions and use-wear reveal hearth-focused activities and a division of the inhabited space into resting and working areas. Site function varied with season of the year: units III-i/j1 and III-i/j2-3 record winter visits focused on filleting and hide processing, while woodworking predominated in unit III-b/d, which subsumes visits to the site over the course of at least one winter, one spring, and one summer. These snapshots of Neandertal behavior match expectations derived from the ethnographic and Upper Paleolithic records for the lifeways of hunter-gatherers inhabiting temperate regions with a markedly seasonal climate.}, }
@article {pmid36394417, year = {2022}, author = {Wielgus, K and Danielewski, M and Walkowiak, J}, title = {Svante Pääbo, reader of the Neanderthal genome.}, journal = {Acta physiologica (Oxford, England)}, volume = {}, number = {}, pages = {e13902}, doi = {10.1111/apha.13902}, pmid = {36394417}, issn = {1748-1716}, }
@article {pmid36375244, year = {2022}, author = {Harvati, K and Reyes-Centeno, H}, title = {Evolution of Homo in the Middle and Late Pleistocene.}, journal = {Journal of human evolution}, volume = {173}, number = {}, pages = {103279}, doi = {10.1016/j.jhevol.2022.103279}, pmid = {36375244}, issn = {1095-8606}, mesh = {Animals ; Humans ; *Hominidae ; Phylogeny ; Biological Evolution ; Fossils ; *Neanderthals ; }, abstract = {The Middle and Late Pleistocene is arguably the most interesting period in human evolution. This broad period witnessed the evolution of our own lineage, as well as that of our sister taxon, the Neanderthals, and related Denisovans. It is exceptionally rich in both fossil and archaeological remains, and uniquely benefits from insights gained through molecular approaches, such as paleogenetics and paleoproteomics, that are currently not widely applicable in earlier contexts. This wealth of information paints a highly complex picture, often described as 'the Muddle in the Middle,' defying the common adage that 'more evidence is needed' to resolve it. Here we review competing phylogenetic scenarios and the historical and theoretical developments that shaped our approaches to the fossil record, as well as some of the many remaining open questions associated with this period. We propose that advancing our understanding of this critical time requires more than the addition of data and will necessitate a major shift in our conceptual and theoretical framework.}, }
@article {pmid36345622, year = {2022}, author = {Tveito, K}, title = {From Icelandic family sagas to Neanderthal genes.}, journal = {Tidsskrift for den Norske laegeforening : tidsskrift for praktisk medicin, ny raekke}, volume = {142}, number = {16}, pages = {}, doi = {10.4045/tidsskr.22.0684}, pmid = {36345622}, issn = {0807-7096}, mesh = {Humans ; Animals ; *Neanderthals/genetics ; Iceland ; }, }
@article {pmid36344982, year = {2022}, author = {Koller, D and Wendt, FR and Pathak, GA and De Lillo, A and De Angelis, F and Cabrera-Mendoza, B and Tucci, S and Polimanti, R}, title = {Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {249}, pmid = {36344982}, issn = {1741-7007}, support = {F32 MH122058/MH/NIMH NIH HHS/United States ; R21 DC018098/DC/NIDCD NIH HHS/United States ; R33 DA047527/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Neanderthals/genetics ; Multifactorial Inheritance ; Genome-Wide Association Study ; Genome, Human ; Asians ; }, abstract = {BACKGROUND: Introgression from extinct Neanderthal and Denisovan human species has been shown to contribute to the genetic pool of modern human populations and their phenotypic spectrum. Evidence of how Neanderthal introgression shaped the genetics of human traits and diseases has been extensively studied in populations of European descent, with signatures of admixture reported for instance in genes associated with pigmentation, immunity, and metabolic traits. However, limited information is currently available about the impact of archaic introgression on other ancestry groups. Additionally, to date, no study has been conducted with respect to the impact of Denisovan introgression on the health and disease of modern populations. Here, we compare the way evolutionary pressures shaped the genetics of complex traits in East Asian and European populations, and provide evidence of the impact of Denisovan introgression on the health of East Asian and Central/South Asian populations.<br><br>RESULTS: Leveraging genome-wide association statistics from the Biobank Japan and UK Biobank, we assessed whether Denisovan and Neanderthal introgression together with other evolutionary genomic signatures were enriched for the heritability of physiological and pathological conditions in populations of East Asian and European descent. In EAS, Denisovan-introgressed loci were enriched for coronary artery disease heritability (1.69-fold enrichment, p=0.003). No enrichment for archaic introgression was observed in EUR. We also performed a phenome-wide association study of Denisovan and Neanderthal alleles in six ancestry groups available in the UK Biobank. In EAS, the Denisovan-introgressed SNP rs62391664 in the major histocompatibility complex region was associated with albumin/globulin ratio (beta=-0.17, p=3.57&#xd7;10[-7]). Neanderthal-introgressed alleles were associated with psychiatric and cognitive traits in EAS (e.g., "No Bipolar or Depression"-rs79043717 beta=-1.5, p=1.1&#xd7;10[-7]), and with blood biomarkers (e.g., alkaline phosphatase-rs11244089 beta=0.1, p=3.69&#xd7;10[-116]) and red hair color (rs60733936 beta=-0.86, p=4.49&#xd7;10[-165]) in EUR. In the other ancestry groups, Neanderthal alleles were associated with several traits, also including the use of certain medications (e.g., Central/South East Asia: indapamide - rs732632 beta=-2.38, p=5.22&#xd7;10[-7]).<br><br>CONCLUSIONS: Our study provides novel evidence regarding the impact of archaic introgression on the genetics of complex traits in worldwide populations, highlighting the specific contribution of Denisovan introgression in EAS populations.}, }
@article {pmid36336759, year = {2022}, author = {Richards, GD and Jabbour, RS and Guipert, G and Defleur, A}, title = {Endocranial anatomy of the Guercy 1 early Neanderthal from Baume Moula-Guercy (Soyons, Ardèche, France).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.25118}, pmid = {36336759}, issn = {1932-8494}, abstract = {We provide the first comparative description of the endocranium of the Guercy 1 Early Neanderthal and examine its affinities to Preneanderthals, Neanderthals, and Homo sapiens. The Guercy 1 cranium derives from deposits chronostratigraphically and biostratigraphically dated to the Eemian Interglacial (MIS 5e). For comparative purposes, we compiled a sample of European and Southwest Asian subadult and adult Middle-to-Late Pleistocene hominins (≈MIS 12-MIS 1; N = 65). We sampled both a Preneanderthal-Neanderthal group and a Homo sapiens group. The Preneanderthal-Neanderthal group was further divided into three time-successive subgroups defined by associated MIS stages. Metric and morphological observations were made on original fossils and physical and virtual endocranial reconstructions. Guercy 1 and other Early Neanderthals, differ from Preneanderthals by increased development of the prefrontal cortex, precentral and postcentral gyri, inferior parietal lobule, and frontoparietal operculum. Early Neanderthal differ, in general, from Late Neanderthals by exhibiting less development in most of the latter brain structures. The late group additionally differentiates itself from the early group by a greater development of the rostral superior parietal lobule, angular gyrus, superior and middle temporal gyri, and caudal branches of the superior temporal gyrus. Endocranial morphology assessed along the Preneanderthal-Neanderthal sequence show that brain structures prominent in Preneanderthals are accentuated in Early-to-Late Neanderthals. However, both the Early and Late groups differentiate themselves by also showing regionally specific changes in brain development. This pattern of morphological change is consistent with a mosaic pattern of neural evolution in these Middle-to-Late Pleistocene hominins.}, }
@article {pmid36323899, year = {2022}, author = {Graham, F}, title = {Daily briefing: First known Neanderthal family discovered.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-022-03378-0}, pmid = {36323899}, issn = {1476-4687}, }
@article {pmid36322514, year = {2022}, author = {Campelo Dos Santos, AL and Owings, A and Sullasi, HSL and Gokcumen, O and DeGiorgio, M and Lindo, J}, title = {Genomic evidence for ancient human migration routes along South America's Atlantic coast.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1986}, pages = {20221078}, pmid = {36322514}, issn = {1471-2954}, support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; History, Ancient ; Animals ; *Human Migration ; Genomics ; Genome, Human ; *Neanderthals ; Brazil ; }, abstract = {An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.}, }
@article {pmid36313404, year = {2022}, author = {Mortazavi, SA and Bevelacqua, JJ and Welsh, JS and Masoumi, SJ and Bahaaddini Beigy Zarandi, BF and Ghadimi-Moghadam, A and Haghani, M and Mortazavi, SMJ}, title = {The Paradox of COVID-19 in Sub-Saharan Africa: Why it is More Unethical Not to Investigate Low Dose Radiotherapy for COVID-19.}, journal = {Journal of biomedical physics &amp; engineering}, volume = {12}, number = {5}, pages = {539-542}, pmid = {36313404}, issn = {2251-7200}, abstract = {An accumulating body of evidence shows that various ethnicities are differentially affected by SARS-COV-2 infection. Moreover, some evidence shows that due to the vaccine inequity and millions of people living with HIV, a major catastrophe could occur in African countries that possibly affects the whole world. Given the possibility that Neanderthal genes confer a slight increase in susceptibility, this difference, at least to some extent, might possibly decrease the risk of the emergence of new SARS-CoV-2 variants among black people in Africa. Recent studies show less death and fewer cases among the ethnic group classified as "Black Africans". Although Neanderthal DNA might explain some differences in morbidity and mortality of COVID-19, a multitude of confounders complicate things to where drawing definite conclusions is hard or even impossible. Using selective-pressure-free treatments (e.g. low dose radiotherapy) for COVID-19 pneumonia would be of crucial importance everywhere, but particularly in sub-Saharan Africa, where "long COVID" in millions of people with HIV paves the road for the more frequent emergence of new variants.}, }
@article {pmid36289417, year = {2022}, author = {Thompson, B and Bundell, S}, title = {Ancient DNA reveals family of Neanderthals living in Siberian cave.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-022-03460-7}, pmid = {36289417}, issn = {1476-4687}, }
@article {pmid36271299, year = {2022}, author = {Vidal-Cordasco, M and Ocio, D and Hickler, T and Marín-Arroyo, AB}, title = {Publisher Correction: Ecosystem productivity affected the spatiotemporal disappearance of Neanderthals in Iberia.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {11}, pages = {1789}, doi = {10.1038/s41559-022-01917-6}, pmid = {36271299}, issn = {2397-334X}, }
@article {pmid36261727, year = {2022}, author = {Callaway, E}, title = {First known Neanderthal family discovered in Siberian cave.}, journal = {Nature}, volume = {610}, number = {7933}, pages = {615-616}, pmid = {36261727}, issn = {1476-4687}, mesh = {Animals ; *Caves ; *Fossils ; *Neanderthals/genetics ; History, Ancient ; }, }
@article {pmid36261548, year = {2022}, author = {Skov, L and Peyrégne, S and Popli, D and Iasi, LNM and Devièse, T and Slon, V and Zavala, EI and Hajdinjak, M and Sümer, AP and Grote, S and Bossoms Mesa, A and López Herráez, D and Nickel, B and Nagel, S and Richter, J and Essel, E and Gansauge, M and Schmidt, A and Korlević, P and Comeskey, D and Derevianko, AP and Kharevich, A and Markin, SV and Talamo, S and Douka, K and Krajcarz, MT and Roberts, RG and Higham, T and Viola, B and Krivoshapkin, AI and Kolobova, KA and Kelso, J and Meyer, M and Pääbo, S and Peter, BM}, title = {Genetic insights into the social organization of Neanderthals.}, journal = {Nature}, volume = {610}, number = {7932}, pages = {519-525}, pmid = {36261548}, issn = {1476-4687}, support = {803147/ERC_/European Research Council/International ; 715069/ERC_/European Research Council/International ; FP7/2007-2013/ERC_/European Research Council/International ; 694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Female ; Humans ; Caves ; Genome/genetics ; Hybridization, Genetic ; *Neanderthals/genetics ; Siberia ; DNA, Mitochondrial/genetics ; Y Chromosome/genetics ; Male ; Family ; Homozygote ; }, abstract = {Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans[1-8], but the social organization of Neanderthal communities remains poorly understood. Here we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave[9,10] and 2 from Okladnikov Cave[11]-making this one of the largest genetic studies of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father-daughter pair and a pair of second-degree relatives, indicating that at least some of the individuals lived at the same time. Up to one-third of these individuals' genomes had long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range.}, }
@article {pmid36261544, year = {2022}, author = {Cassidy, LM}, title = {The first genomic portrait of a Neanderthal family.}, journal = {Nature}, volume = {610}, number = {7932}, pages = {454-455}, pmid = {36261544}, issn = {1476-4687}, mesh = {Animals ; *Neanderthals/genetics ; Genome/genetics ; Genomics ; }, }
@article {pmid36261474, year = {2022}, author = {Mayoral, E and Duveau, J and Santos, A and Ramírez, AR and Morales, JA and Díaz-Delgado, R and Rivera-Silva, J and Gómez-Olivencia, A and Díaz-Martínez, I}, title = {New dating of the Matalascañas footprints provides new evidence of the Middle Pleistocene (MIS 9-8) hominin paleoecology in southern Europe.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17505}, pmid = {36261474}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Hominidae ; Fossils ; *Neanderthals ; Europe ; Luminescence ; }, abstract = {Hominin footprints were recently discovered at Matalascañas (Huelva; South of Iberian Peninsula). They were dated thanks to a previous study in deposits of the Asperillo cliff to 106 ± 19 ka, Upper Pleistocene, making Neandertals the most likely track-makers. In this paper, we report new Optically Stimulated Luminescence dating that places the hominin footprints surface in the range of 295.8 ± 17 ka (MIS 9-MIS 8 transition, Middle Pleistocene). This new age implies that the possible track-makers are individuals more likely from the Neandertal evolutionary lineage. Regardless of the taxon attributed to the Matalascañas footprints, they supplement the existing partial fossil record for the European Middle Pleistocene Hominins being notably the first palaeoanthropological evidence (hominin skeleton or footprints) from the MIS 9 and MIS 8 transition discovered in the Iberian Peninsula, a moment of climatic evolution from warm to cool. Thus, the Matalascañas footprints represent a crucial record for understanding human occupations in Europe in the Pleistocene.}, }
@article {pmid36253794, year = {2022}, author = {Bergman, J and Schierup, MH}, title = {Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {215}, pmid = {36253794}, issn = {1474-760X}, mesh = {Animals ; Female ; *Hominidae/genetics ; Humans ; Male ; Nucleotides ; *Pseudoautosomal Regions ; Receptor, PAR-1/genetics ; Y Chromosome/genetics ; }, abstract = {BACKGROUND: The pseudoautosomal region 1 (PAR1) is a 2.7 Mb telomeric region of human sex chromosomes. PAR1 has a crucial role in ensuring proper segregation of sex chromosomes during male meiosis, exposing it to extreme recombination and mutation processes. We investigate PAR1 evolution using population genomic datasets of extant humans, eight populations of great apes, and two archaic human genome sequences.<br><br>RESULTS: We find that PAR1 is fast evolving and closer to evolutionary nucleotide equilibrium than autosomal telomeres. We detect a difference between substitution patterns and extant diversity in PAR1, mainly driven by the conflict between strong mutation and recombination-associated fixation bias at CpG sites. We detect excess C-to-G mutations in PAR1 of all great apes, specific to the mutagenic effect of male recombination. Despite recent evidence for Y chromosome introgression from humans into Neanderthals, we find that the Neanderthal PAR1 retained similarity to the Denisovan sequence. We find differences between substitution spectra of these archaics suggesting rapid evolution of PAR1 in recent hominin history. Frequency analysis of alleles segregating in females and males provided no evidence for recent sexual antagonism in this region. We study repeat content and double-strand break hotspot regions in PAR1 and find that they may play roles in ensuring the obligate X-Y recombination event during male meiosis.<br><br>CONCLUSIONS: Our study provides an unprecedented quantification of population genetic forces governing PAR1 biology across extant and extinct hominids. PAR1 evolutionary dynamics are predominantly governed by recombination processes with a strong impact on mutation patterns across all species.}, }
@article {pmid36252021, year = {2022}, author = {Jaouen, K and Villalba-Mouco, V and Smith, GM and Trost, M and Leichliter, J and Lüdecke, T and Méjean, P and Mandrou, S and Chmeleff, J and Guiserix, D and Bourgon, N and Blasco, F and Mendes Cardoso, J and Duquenoy, C and Moubtahij, Z and Salazar Garcia, DC and Richards, M and Tütken, T and Hublin, JJ and Utrilla, P and Montes, L}, title = {A Neandertal dietary conundrum: Insights provided by tooth enamel Zn isotopes from Gabasa, Spain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {43}, pages = {e2109315119}, pmid = {36252021}, issn = {1091-6490}, mesh = {Animals ; Carbon/analysis ; Carbon Isotopes/analysis ; *Carnivora ; Collagen ; Dental Enamel/chemistry ; Diet ; *Neanderthals ; Nitrogen Isotopes/analysis ; Oxygen/analysis ; Spain ; Strontium/analysis ; *Tooth/chemistry ; *Trace Elements/analysis ; Zinc/analysis ; Zinc Isotopes/analysis ; }, abstract = {The characterization of Neandertals' diets has mostly relied on nitrogen isotope analyses of bone and tooth collagen. However, few nitrogen isotope data have been recovered from bones or teeth from Iberia due to poor collagen preservation at Paleolithic sites in the region. Zinc isotopes have been shown to be a reliable method for reconstructing trophic levels in the absence of organic matter preservation. Here, we present the results of zinc (Zn), strontium (Sr), carbon (C), and oxygen (O) isotope and trace element ratio analysis measured in dental enamel on a Pleistocene food web in Gabasa, Spain, to characterize the diet and ecology of a Middle Paleolithic Neandertal individual. Based on the extremely low δ[66]Zn value observed in the Neandertal's tooth enamel, our results support the interpretation of Neandertals as carnivores as already suggested by δ[15]N isotope values of specimens from other regions. Further work could help identify if such isotopic peculiarities (lowest δ[66]Zn and highest δ[15]N of the food web) are due to a metabolic and/or dietary specificity of the Neandertals.}, }
@article {pmid36229473, year = {2022}, author = {Djakovic, I and Key, A and Soressi, M}, title = {Optimal linear estimation models predict 1400-2900 years of overlap between Homo sapiens and Neandertals prior to their disappearance from France and northern Spain.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15000}, pmid = {36229473}, issn = {2045-2322}, mesh = {Animals ; Bayes Theorem ; Fossils ; France ; *Hominidae ; Humans ; *Neanderthals ; Spain ; }, abstract = {Recent fossil discoveries suggest that Neandertals and Homo sapiens may have co-existed in Europe for as long as 5 to 6000 years. Yet, evidence for their contemporaneity at any regional scale remains highly elusive. In France and northern Spain, a region which features some of the latest directly-dated Neandertals in Europe, Protoaurignacian assemblages attributed to Homo sapiens appear to 'replace' Neandertal-associated Châtelperronian assemblages. Using the earliest and latest known occurrences as starting points, Bayesian modelling has provided indication that these occupations may in fact have been partly contemporaneous. The reality, however, is that we are unlikely to ever identify the 'first' or 'last' appearance of a species or cultural tradition in the archaeological and fossil record. Here, we use optimal linear estimation modelling to estimate the first appearance date of Homo sapiens and the extinction date of Neandertals in France and northern Spain by statistically inferring these 'missing' portions of the Protoaurignacian and Châtelperronian archaeological records. Additionally, we estimate the extinction date of Neandertals in this region using a dataset of directly-dated Neandertal fossil remains. Our total dataset consists of sixty-six modernly produced radiocarbon determinations which we recalibrated using the newest calibration curve (IntCal20) to produce updated age ranges. The results suggest that the onset of the Homo sapiens occupation of this region likely preceded the extinction of Neandertals and the Châtelperronian by up to 1400-2900 years. This reaffirms the Bayesian-derived duration of co-existence between these groups during the initial Upper Palaeolithic of this region using a novel independent method, and indicates that our understanding of the timing of these occupations may not be suffering from substantial gaps in the record. Whether or not this co-existence featured some form of direct interaction, however, remains to be resolved.}, }
@article {pmid36207518, year = {2022}, author = {Callaway, E}, title = {From Neanderthal genome to Nobel prize: meet geneticist Svante Pääbo.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {36207518}, issn = {1476-4687}, }
@article {pmid36198681, year = {2022}, author = {Dannemann, M and Milaneschi, Y and Yermakovich, D and Stiglbauer, V and Kariis, HM and Krebs, K and Friese, MA and Otte, C and ,  and Lehto, K and Penninx, BWJH and Kelso, J and Gold, SM}, title = {Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes.}, journal = {Translational psychiatry}, volume = {12}, number = {1}, pages = {433}, pmid = {36198681}, issn = {2158-3188}, support = {RC2 MH089951/MH/NIMH NIH HHS/United States ; RC2 MH089995/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Genetic Variation ; Genome ; Haplotypes ; Humans ; *Neanderthals/genetics ; Phenotype ; }, abstract = {Despite advances in identifying the genetic basis of psychiatric and neurological disorders, fundamental questions about their evolutionary origins remain elusive. Here, introgressed variants from archaic humans such as Neandertals can serve as an intriguing research paradigm. We compared the number of associations for Neandertal variants to the number of associations of frequency-matched non-archaic variants with regard to human CNS disorders (neurological and psychiatric), nervous system drug prescriptions (as a proxy for disease), and related, non-disease phenotypes in the UK biobank (UKBB). While no enrichment for Neandertal genetic variants were observed in the UKBB for psychiatric or neurological disease categories, we found significant associations with certain behavioral phenotypes including pain, chronotype/sleep, smoking and alcohol consumption. In some instances, the enrichment signal was driven by Neandertal variants that represented the strongest association genome-wide. SNPs within a Neandertal haplotype that was associated with smoking in the UKBB could be replicated in four independent genomics datasets.Our data suggest that evolutionary processes in recent human evolution like admixture with Neandertals significantly contribute to behavioral phenotypes but not psychiatric and neurological diseases. These findings help to link genetic variants in a population to putative past beneficial effects, which likely only indirectly contribute to pathology in modern day humans.}, }
@article {pmid36181428, year = {2022}, author = {Huang, X and Kruisz, P and Kuhlwilm, M}, title = {sstar: A Python Package for Detecting Archaic Introgression from Population Genetic Data with S.}, journal = {Molecular biology and evolution}, volume = {39}, number = {11}, pages = {}, pmid = {36181428}, issn = {1537-1719}, mesh = {Humans ; Animals ; *Genome, Human ; *Neanderthals/genetics ; Genetics, Population ; }, abstract = {S* is a widely used statistic for detecting archaic admixture from population genetic data. Previous studies used freezing-archer to apply S*, which is only directly applicable to the specific case of Neanderthal and Denisovan introgression in Papuans. Here, we implemented sstar for a more general purpose. Compared with several tools, including SPrime, SkovHMM, and ArchaicSeeker2.0, for detecting introgressed fragments with simulations, our results suggest that sstar is robust to differences in demographic models, including ghost introgression and two-source introgression. We believe sstar will be a useful tool for detecting introgressed fragments in various scenarios and in non-human species.}, }
@article {pmid36175541, year = {2022}, author = {Vidal-Cordasco, M and Ocio, D and Hickler, T and Marín-Arroyo, AB}, title = {Ecosystem productivity affected the spatiotemporal disappearance of Neanderthals in Iberia.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {11}, pages = {1644-1657}, pmid = {36175541}, issn = {2397-334X}, mesh = {Humans ; Animals ; *Neanderthals ; Ecosystem ; Bayes Theorem ; }, abstract = {What role did fluctuations play in biomass availability for secondary consumers in the disappearance of Neanderthals and the survival of modern humans? To answer this, we quantify the effects of stadial and interstadial conditions on ecosystem productivity and human spatiotemporal distribution patterns during the Middle to Upper Palaeolithic transition (50,000-30,000 calibrated years before the present) in Iberia. First, we used summed probability distribution, optimal linear estimation and Bayesian age modelling to reconstruct an updated timescale for the transition. Next, we executed a generalized dynamic vegetation model to estimate the net primary productivity. Finally, we developed a macroecological model validated with present-day observations to calculate herbivore abundance. The results indicate that, in the Eurosiberian region, the disappearance of Neanderthal groups was contemporaneous with a significant decrease in the available biomass for secondary consumers, and the arrival of the first Homo sapiens populations coincided with an increase in herbivore carrying capacity. During stadials, the Mediterranean region had the most stable conditions and the highest biomass of medium and medium-large herbivores. These outcomes support an ecological cause for the hiatus between the Mousterian and Aurignacian technocomplexes in Northern Iberia and the longer persistence of Neanderthals in southern latitudes.}, }
@article {pmid36167050, year = {2022}, author = {Reilly, PF and Tjahjadi, A and Miller, SL and Akey, JM and Tucci, S}, title = {The contribution of Neanderthal introgression to modern human traits.}, journal = {Current biology : CB}, volume = {32}, number = {18}, pages = {R970-R983}, doi = {10.1016/j.cub.2022.08.027}, pmid = {36167050}, issn = {1879-0445}, support = {R35 GM147565/GM/NIGMS NIH HHS/United States ; R01 GM110068/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa ; Alleles ; Animals ; Biological Evolution ; Genome, Human ; Humans ; *Neanderthals/genetics ; }, abstract = {Neanderthals, our closest extinct relatives, lived in western Eurasia from 400,000 years ago until they went extinct around 40,000 years ago. DNA retrieved from ancient specimens revealed that Neanderthals mated with modern human contemporaries. As a consequence, introgressed Neanderthal DNA survives scattered across the human genome such that 1-4% of the genome of present-day people outside Africa are inherited from Neanderthal ancestors. Patterns of Neanderthal introgressed genomic sequences suggest that Neanderthal alleles had distinct fates in the modern human genetic background. Some Neanderthal alleles facilitated human adaptation to new environments such as novel climate conditions, UV exposure levels and pathogens, while others had deleterious consequences. Here, we review the body of work on Neanderthal introgression over the past decade. We describe how evolutionary forces shaped the genomic landscape of Neanderthal introgression and highlight the impact of introgressed alleles on human biology and phenotypic variation.}, }
@article {pmid36162354, year = {2022}, author = {Lockey, AL and Rodríguez, L and Martín-Francés, L and Arsuaga, JL and Bermúdez de Castro, JM and Crété, L and Martinón-Torres, M and Parfitt, S and Pope, M and Stringer, C}, title = {Comparing the Boxgrove and Atapuerca (Sima de los Huesos) human fossils: Do they represent distinct paleodemes?.}, journal = {Journal of human evolution}, volume = {172}, number = {}, pages = {103253}, doi = {10.1016/j.jhevol.2022.103253}, pmid = {36162354}, issn = {1095-8606}, mesh = {Animals ; Adult ; Humans ; Fossils ; Cross-Sectional Studies ; *Hominidae/anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology ; Tibia/anatomy &amp; histology ; Spain ; }, abstract = {The early Middle Pleistocene human material from Boxgrove (West Sussex, UK) consists of a partial left tibia and two lower incisors from a separate adult individual. These remains derive from deposits assigned to the MIS 13 interglacial at about 480 ka and have been referred to as Homo cf. heidelbergensis. The much larger skeletal sample from the Sima de los Huesos (Atapuerca, Spain) is dated to the succeeding MIS 12, at about 430 ka. This fossil material has previously been assigned to Homo heidelbergensis but is now placed within the Neanderthal clade. Because of the scarcity of human remains from the Middle Pleistocene and their morphological variability, this study assessed whether the Boxgrove specimens fit within the morphological variability of the homogeneous Sima de los Huesos population. Based on morphometric analyses performed against 22 lower incisors from Sima de los Huesos and published material, the data from the Boxgrove incisors place them comfortably within the range of Sima de los Huesos. Both assemblages present robust incisors distinct from the overall small recent Homo sapiens incisors, and Boxgrove also aligns closely with Homo neanderthalensis and some other European Middle Pleistocene hominins. Following morphological and cross-sectional analyses of the Boxgrove tibia compared to seven adult Sima de los Huesos specimens and a set of comparative tibiae, Boxgrove is shown to be similar to Sima de los Huesos and Neanderthals in having thick cortices and bone walls, but in contrast resembles modern humans in having a straight anterior tibial crest and a suggestion of a lateral concavity. Based on the patterns observed, there is no justification for assigning the Boxgrove and Sima de los Huesos incisors to distinct paleodemes, but the tibial data show greater contrasts and suggest that all three of these samples are unlikely to represent the same paleodeme.}, }
@article {pmid36161899, year = {2022}, author = {Alagöz, G and Molz, B and Eising, E and Schijven, D and Francks, C and Stein, JL and Fisher, SE}, title = {Using neuroimaging genomics to investigate the evolution of human brain structure.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2200638119}, pmid = {36161899}, issn = {1091-6490}, support = {R01 DC016977/DC/NIDCD NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Brain/growth &amp; development/ultrastructure ; DNA, Ancient ; *Genomics/methods ; Humans ; *Neuroimaging/methods ; *Polymorphism, Single Nucleotide ; }, abstract = {Alterations in brain size and organization represent some of the most distinctive changes in the emergence of our species. Yet, there is limited understanding of how genetic factors contributed to altered neuroanatomy during human evolution. Here, we analyze neuroimaging and genetic data from up to 30,000 people in the UK Biobank and integrate with genomic annotations for different aspects of human evolution, including those based on ancient DNA and comparative genomics. We show that previously reported signals of recent polygenic selection for cortical anatomy are not replicable in a more ancestrally homogeneous sample. We then investigate relationships between evolutionary annotations and common genetic variants shaping cortical surface area and white-matter connectivity for each hemisphere. Our analyses identify single-nucleotide polymorphism heritability enrichment in human-gained regulatory elements that are active in early brain development, affecting surface areas of several parts of the cortex, including left-hemispheric speech-associated regions. We also detect heritability depletion in genomic regions with Neanderthal ancestry for connectivity of the uncinate fasciculus; this is a white-matter tract involved in memory, language, and socioemotional processing with relevance to neuropsychiatric disorders. Finally, we show that common genetic loci associated with left-hemispheric pars triangularis surface area overlap with a human-gained enhancer and affect regulation of ZIC4, a gene implicated in neurogenesis. This work demonstrates how genomic investigations of present-day neuroanatomical variation can help shed light on the complexities of our evolutionary past.}, }
@article {pmid36151242, year = {2022}, author = {Sossa-Ríos, S and Mayor, A and Hernández, CM and Bencomo, M and Pérez, L and Galván, B and Mallol, C and Vaquero, M}, title = {Multidisciplinary evidence of an isolated Neanderthal occupation in Abric del Pastor (Alcoi, Iberian Peninsula).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15883}, pmid = {36151242}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Clergy ; Fossils ; Humans ; *Neanderthals ; Occupations ; *Starlings ; }, abstract = {Testing Neanderthal behavioural hypotheses requires a spatial-temporal resolution to the level of a human single occupation episode. Yet, most of the behavioural data on Neanderthals has been obtained from coarsely dated, time-averaged contexts affected by the archaeological palimpsest effect and a diversity of postdepositional processes. This implies that time-resolved Neanderthal behaviour remains largely unknown. In this study, we performed archaeostratigraphic analysis on stratigraphic units IVe, IVf, IVg, Va, Vb and Vc from Abric del Pastor (Alcoi, Iberian Peninsula). Further, we isolated the archaeological remains associated with the resulting archaeostratigraphic unit and applied raw material, technological, use-wear, archaeozoological and spatial analyses. Our results show a low-density accumulation of remains from flintknapping, flint tool-use and animal processing around a hearth. These data provide a time-resolved human dimension to previous high-resolution environmental and pyrotechnological data on the same hearth, representing the first comprehensive characterisation of a Neanderthal single occupation episode. Our integrated, multidisciplinary method also contributes to advance our understanding of archaeological record formation processes.}, }
@article {pmid36138831, year = {2022}, author = {Garralda, MD and Weiner, S and Arensburg, B and Maureille, B and Vandermeersch, B}, title = {Dental Paleobiology in a Juvenile Neanderthal (Combe-Grenal, Southwestern France).}, journal = {Biology}, volume = {11}, number = {9}, pages = {}, pmid = {36138831}, issn = {2079-7737}, abstract = {Combe-Grenal site (Southwest France) was excavated by F. Bordes between 1953 and 1965. He found several human remains in Mousterian levels 60, 39, 35 and especially 25, corresponding to MIS 4 (~75-70/60 ky BP) and with Quina Mousterian lithics. One of the fossils found in level 25 is Combe-Grenal IV, consisting of a fragment of the left corpus of a juvenile mandible. This fragment displays initial juvenile periodontitis, and the two preserved teeth (LLP4 and LLM1) show moderate attrition and dental calculus. The SEM tartar analysis demonstrates the presence of cocci and filamentous types of bacteria, the former being more prevalent. This result is quite different from those obtained for the two adult Neanderthals Kebara 2 and Subalyuk 1, where more filamentous bacteria appear, especially in the Subalyuk 1 sample from Central Europe. These findings agree with the available biomedical data on periodontitis and tartar development in extant individuals, despite the different environmental conditions and diets documented by numerous archeological, taphonomical and geological data available on Neanderthals and present-day populations. New metagenomic analyses are extending this information, and despite the inherent difficulties, they will open important perspectives in studying this ancient human pathology.}, }
@article {pmid36107211, year = {2022}, author = {Ruf, CG and Schmidt, S and Kliesch, S and Oing, C and Pfister, D and Busch, J and Heinzelbecker, J and Winter, C and Zengerling, F and Albers, P and Oechsle, K and Krege, S and Lackner, J and Dieckmann, KP}, title = {Testicular germ cell tumours' clinical stage I: comparison of surveillance with adjuvant treatment strategies regarding recurrence rates and overall survival-a systematic review.}, journal = {World journal of urology}, volume = {40}, number = {12}, pages = {2889-2900}, pmid = {36107211}, issn = {1433-8726}, mesh = {Male ; Young Adult ; Humans ; Orchiectomy/methods ; Neoplasm Staging ; Neoplasm Recurrence, Local/therapy/drug therapy ; *Testicular Neoplasms/pathology ; *Neoplasms, Germ Cell and Embryonal/pathology ; *Seminoma/pathology ; Lymph Node Excision/methods ; Chemotherapy, Adjuvant/methods ; }, abstract = {PURPOSE: Testicular germ cell tumours (GCTs) represent the most common malignancy in young adult males with two thirds of all cases presenting with clinical stage I (CSI). Active surveillance is the management modality mostly favoured by current guidelines. This systematic review assesses the treatment results in CSI patients concerning recurrence rate and overall survival in non-seminoma (NS) and pure seminoma (SE) resulting from surveillance in comparison to adjuvant strategies.<br><br>METHODS/SYSTEMATIC REVIEW: We performed a systematic literature review confining the search to most recent studies published 2010-2021 that reported direct comparisons of surveillance to adjuvant management. We searched Medline and the Cochrane Library with additional hand-searching of reference lists to identify relevant studies. Data extraction and quality assessment of included studies were performed with stratification for histology (NS vs. SE) and treatment modalities. The results were tabulated and evaluated with descriptive statistical methods.<br><br>RESULTS: Thirty-four studies met the inclusion criteria. In NS patients relapse rates were 12 to 37%, 0 to 10%, and 0 to 11.8% for surveillance, chemotherapy and for retroperitoneal lymph node dissection (RPLND) while overall survival rates were 90.7-100%, 91.7-100%, and 97-99.1%, respectively. In SE CSI, relapse rates were 0-22.3%, 0-5%, and 0-12.5% for surveillance, radiotherapy, chemotherapy, while overall survival rates were 84.1-98.7%, 83.5-100%, and 92.3-100%, respectively.<br><br>CONCLUSION: In both histologic subgroups, active surveillance offers almost identical overall survival as adjuvant management strategies, however, at the expense of higher relapse rates. Each of the management strategies in CSI GCT patients have specific merits and shared-decision-making is advised to tailor treatment.}, }
@article {pmid36097061, year = {2022}, author = {Graham, F}, title = {Daily briefing: Mutation might have given us a cognitive advantage over Neanderthals.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-022-02913-3}, pmid = {36097061}, issn = {1476-4687}, }
@article {pmid36074851, year = {2022}, author = {Pinson, A and Xing, L and Namba, T and Kalebic, N and Peters, J and Oegema, CE and Traikov, S and Reppe, K and Riesenberg, S and Maricic, T and Derihaci, R and Wimberger, P and Pääbo, S and Huttner, WB}, title = {Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals.}, journal = {Science (New York, N.Y.)}, volume = {377}, number = {6611}, pages = {eabl6422}, doi = {10.1126/science.abl6422}, pmid = {36074851}, issn = {1095-9203}, mesh = {Animals ; Ependymoglial Cells/cytology ; Ferrets ; Humans ; Mice ; *Neanderthals/embryology/genetics ; *Neocortex/embryology ; *Neurogenesis/genetics/physiology ; *Transketolase/genetics/metabolism ; }, abstract = {Neanderthal brains were similar in size to those of modern humans. We sought to investigate potential differences in neurogenesis during neocortex development. Modern human transketolase-like 1 (TKTL1) differs from Neanderthal TKTL1 by a lysine-to-arginine amino acid substitution. Using overexpression in developing mouse and ferret neocortex, knockout in fetal human neocortical tissue, and genome-edited cerebral organoids, we found that the modern human variant, hTKTL1, but not the Neanderthal variant, increases the abundance of basal radial glia (bRG) but not that of intermediate progenitors (bIPs). bRG generate more neocortical neurons than bIPs. The hTKTL1 effect requires the pentose phosphate pathway and fatty acid synthesis. Inhibition of these metabolic pathways reduces bRG abundance in fetal human neocortical tissue. Our data suggest that neocortical neurogenesis in modern humans differs from that in Neanderthals.}, }
@article {pmid36064759, year = {2022}, author = {Harvati, K and Ackermann, RR}, title = {Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {10}, pages = {1573-1585}, pmid = {36064759}, issn = {2397-334X}, mesh = {Animals ; DNA, Ancient ; Fossils ; *Hominidae/anatomy &amp; histology/genetics ; Humans ; Hybridization, Genetic ; Mammals/genetics ; *Neanderthals/genetics ; }, abstract = {Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.}, }
@article {pmid36044840, year = {2022}, author = {Kaczanowska, J and Ganglberger, F and Chernomor, O and Kargl, D and Galik, B and Hess, A and Moodley, Y and von Haeseler, A and Bühler, K and Haubensak, W}, title = {Molecular archaeology of human cognitive traits.}, journal = {Cell reports}, volume = {40}, number = {9}, pages = {111287}, doi = {10.1016/j.celrep.2022.111287}, pmid = {36044840}, issn = {2211-1247}, mesh = {Animals ; Archaeology ; Cognition/physiology ; Evolution, Molecular ; Genome, Human ; *Hominidae/genetics ; Humans ; Mammals ; *Neanderthals/genetics ; Phenotype ; }, abstract = {The brains and minds of our human ancestors remain inaccessible for experimental exploration. Therefore, we reconstructed human cognitive evolution by projecting nonsynonymous/synonymous rate ratios (ω values) in mammalian phylogeny onto the anatomically modern human (AMH) brain. This atlas retraces human neurogenetic selection and allows imputation of ancestral evolution in task-related functional networks (FNs). Adaptive evolution (high ω values) is associated with excitatory neurons and synaptic function. It shifted from FNs for motor control in anthropoid ancestry (60-41 mya) to attention in ancient hominoids (26-19 mya) and hominids (19-7.4 mya). Selection in FNs for language emerged with an early hominin ancestor (7.4-1.7 mya) and was later accompanied by adaptive evolution in FNs for strategic thinking during recent (0.8 mya-present) speciation of AMHs. This pattern mirrors increasingly complex cognitive demands and suggests that co-selection for language alongside strategic thinking may have separated AMHs from their archaic Denisovan and Neanderthal relatives.}, }
@article {pmid36009790, year = {2022}, author = {Churchill, SE and Keys, K and Ross, AH}, title = {Midfacial Morphology and Neandertal-Modern Human Interbreeding.}, journal = {Biology}, volume = {11}, number = {8}, pages = {}, pmid = {36009790}, issn = {2079-7737}, abstract = {Ancient DNA from, Neandertal and modern human fossils, and comparative morphological analyses of them, reveal a complex history of interbreeding between these lineages and the introgression of Neandertal genes into modern human genomes. Despite substantial increases in our knowledge of these events, the timing and geographic location of hybridization events remain unclear. Six measures of facial size and shape, from regional samples of Neandertals and early modern humans, were used in a multivariate exploratory analysis to try to identify regions in which early modern human facial morphology was more similar to that of Neandertals, which might thus represent regions of greater introgression of Neandertal genes. The results of canonical variates analysis and hierarchical cluster analysis suggest important affinities in facial morphology between both Middle and Upper Paleolithic early modern humans of the Near East with Neandertals, highlighting the importance of this region for interbreeding between the two lineages.}, }
@article {pmid35998220, year = {2022}, author = {Eising, E and Mirza-Schreiber, N and de Zeeuw, EL and Wang, CA and Truong, DT and Allegrini, AG and Shapland, CY and Zhu, G and Wigg, KG and Gerritse, ML and Molz, B and Alagöz, G and Gialluisi, A and Abbondanza, F and Rimfeld, K and van Donkelaar, M and Liao, Z and Jansen, PR and Andlauer, TFM and Bates, TC and Bernard, M and Blokland, K and Bonte, M and Børglum, AD and Bourgeron, T and Brandeis, D and Ceroni, F and Csépe, V and Dale, PS and de Jong, PF and DeFries, JC and Démonet, JF and Demontis, D and Feng, Y and Gordon, SD and Guger, SL and Hayiou-Thomas, ME and Hernández-Cabrera, JA and Hottenga, JJ and Hulme, C and Kere, J and Kerr, EN and Koomar, T and Landerl, K and Leonard, GT and Lovett, MW and Lyytinen, H and Martin, NG and Martinelli, A and Maurer, U and Michaelson, JJ and Moll, K and Monaco, AP and Morgan, AT and Nöthen, MM and Pausova, Z and Pennell, CE and Pennington, BF and Price, KM and Rajagopal, VM and Ramus, F and Richer, L and Simpson, NH and Smith, SD and Snowling, MJ and Stein, J and Strug, LJ and Talcott, JB and Tiemeier, H and van der Schroeff, MP and Verhoef, E and Watkins, KE and Wilkinson, M and Wright, MJ and Barr, CL and Boomsma, DI and Carreiras, M and Franken, MJ and Gruen, JR and Luciano, M and Müller-Myhsok, B and Newbury, DF and Olson, RK and Paracchini, S and Paus, T and Plomin, R and Reilly, S and Schulte-Körne, G and Tomblin, JB and van Bergen, E and Whitehouse, AJO and Willcutt, EG and St Pourcain, B and Francks, C and Fisher, SE}, title = {Genome-wide analyses of individual differences in quantitatively assessed reading- and language-related skills in up to 34,000 people.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {35}, pages = {e2202764119}, pmid = {35998220}, issn = {1091-6490}, support = {U01 DA051039/DA/NIDA NIH HHS/United States ; R01 DC014489/DC/NIDCD NIH HHS/United States ; U01 DA051038/DA/NIDA NIH HHS/United States ; RC2 MH089924/MH/NIMH NIH HHS/United States ; U01 DA051037/DA/NIDA NIH HHS/United States ; U01 DA051016/DA/NIDA NIH HHS/United States ; U01 MH109514/MH/NIMH NIH HHS/United States ; U01 DA041106/DA/NIDA NIH HHS/United States ; U01 DA041148/DA/NIDA NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; RC2 MH089983/MH/NIMH NIH HHS/United States ; U24 DA041147/DA/NIDA NIH HHS/United States ; P50 HD027802/HD/NICHD NIH HHS/United States ; U01 DA041120/DA/NIDA NIH HHS/United States ; RC2 MH089995/MH/NIMH NIH HHS/United States ; U01 DA051018/DA/NIDA NIH HHS/United States ; K99 HD094902/HD/NICHD NIH HHS/United States ; U01 DA041093/DA/NIDA NIH HHS/United States ; R01 DC016977/DC/NIDCD NIH HHS/United States ; EP-C-15-001/EPA/EPA/United States ; U24 DA041123/DA/NIDA NIH HHS/United States ; U01 DA041134/DA/NIDA NIH HHS/United States ; U01 DA041022/DA/NIDA NIH HHS/United States ; R01 AG046938/AG/NIA NIH HHS/United States ; R01 MH058799/MH/NIMH NIH HHS/United States ; U01 DA041156/DA/NIDA NIH HHS/United States ; U01 DA050987/DA/NIDA NIH HHS/United States ; U01 DA041025/DA/NIDA NIH HHS/United States ; U01 DA050989/DA/NIDA NIH HHS/United States ; R01 NS043530/NS/NINDS NIH HHS/United States ; U01 DA050988/DA/NIDA NIH HHS/United States ; U24 MH068457/MH/NIMH NIH HHS/United States ; U01 DA041089/DA/NIDA NIH HHS/United States ; U01 DA041117/DA/NIDA NIH HHS/United States ; U01 DA041028/DA/NIDA NIH HHS/United States ; U01 DA041048/DA/NIDA NIH HHS/United States ; U01 DA041174/DA/NIDA NIH HHS/United States ; RC2 DA029475/DA/NIDA NIH HHS/United States ; 105621/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; 204821/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 217065/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; MOP-82893//CIHR/Canada ; 076566/WT_/Wellcome Trust/United Kingdom ; G1000569/MRC_/Medical Research Council/United Kingdom ; MR/V012878/MRC_/Medical Research Council/United Kingdom ; MR/M021475/1/MRC_/Medical Research Council/United Kingdom ; MOP-133440//CIHR/Canada ; 076566/Z/05/Z/WT_/Wellcome Trust/United Kingdom ; 075491/Z/04/WT_/Wellcome Trust/United Kingdom ; 082036/B/07/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Genetic Loci ; *Genome-Wide Association Study ; Humans ; *Individuality ; Language ; Polymorphism, Single Nucleotide ; *Reading ; *Speech ; Young Adult ; }, abstract = {The use of spoken and written language is a fundamental human capacity. Individual differences in reading- and language-related skills are influenced by genetic variation, with twin-based heritability estimates of 30 to 80% depending on the trait. The genetic architecture is complex, heterogeneous, and multifactorial, but investigations of contributions of single-nucleotide polymorphisms (SNPs) were thus far underpowered. We present a multicohort genome-wide association study (GWAS) of five traits assessed individually using psychometric measures (word reading, nonword reading, spelling, phoneme awareness, and nonword repetition) in samples of 13,633 to 33,959 participants aged 5 to 26 y. We identified genome-wide significant association with word reading (rs11208009, P = 1.098 × 10[-8]) at a locus that has not been associated with intelligence or educational attainment. All five reading-/language-related traits showed robust SNP heritability, accounting for 13 to 26% of trait variability. Genomic structural equation modeling revealed a shared genetic factor explaining most of the variation in word/nonword reading, spelling, and phoneme awareness, which only partially overlapped with genetic variation contributing to nonword repetition, intelligence, and educational attainment. A multivariate GWAS of word/nonword reading, spelling, and phoneme awareness maximized power for follow-up investigation. Genetic correlation analysis with neuroimaging traits identified an association with the surface area of the banks of the left superior temporal sulcus, a brain region linked to the processing of spoken and written language. Heritability was enriched for genomic elements regulating gene expression in the fetal brain and in chromosomal regions that are depleted of Neanderthal variants. Together, these results provide avenues for deciphering the biological underpinnings of uniquely human traits.}, }
@article {pmid35976853, year = {2022}, author = {Vettese, D and Borel, A and Blasco, R and Chevillard, L and Stavrova, T and Thun Hohenstein, U and Arzarello, M and Moncel, MH and Daujeard, C}, title = {New evidence of Neandertal butchery traditions through the marrow extraction in southwestern Europe (MIS 5-3).}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0271816}, pmid = {35976853}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; Bone Marrow ; Bone and Bones ; Europe ; Fossils ; Humans ; *Neanderthals ; Technology ; Vegetables ; }, abstract = {Long bone breakage for bone marrow recovery is a commonly observed practice in Middle Palaeolithic contexts, regardless of the climatic conditions. While lithic technology is largely used to define cultural patterns in human groups, despite dedicating research by zooarchaeologists, for now butchering techniques rarely allowed the identification of clear traditions, notably for ancient Palaeolithic periods. In this paper, we test the hypothesis of butchery traditions among Neandertal groupsusing the bone assemblages from three sites in southwestern Europe. These sites are located in southeastern France and northern Italy and are dated to the Late Middle Palaeolithic: Abri du Maras (Marine Isotopic Stages (MIS) 4-3, Ardèche), Saint-Marcel (MIS 3, Ardèche), and Riparo Tagliente (MIS 4-3, Verona). The detection of culturally-induced patterns of bone breakage involves differentiating them from intuitively generated patterns. To tackle this issue, we used a zooarchaeological approach focusing on the percussion marks produced during the bone breakage process. Statistical analyses as the chi-square test of independence were employed to verify if percussion mark locations were randomly distributed, and if these distributions were different from the intuitive ones. For femurs and humeri, our results demonstrate that Neandertal groups occupying the Abri du Maras (levels 4.1 and 4.2) and the Saint-Marcel Cave (levels g and h) sites in France applied butchery traditions to recover yellow marrow. However, the traditions developed at each site were different. On the contrary, in Riparo Tagliente, in Italy, several groups or individuals of a same group did not share the same butchery traditions over time. Regarding the Abri du Maras and Saint Marcel Cave assemblages, our research demonstrates that Neandertal groups applied intense standardized bone breakage, far from the intuitive practice observed experimentally and related to bone density and/or skeletal morphology. These standardized patterns, which are systematic and counter-intuitive, can be interpreted as culturally induced for the Abri du Maras and Saint Marcel Cave. The diversity of Neandertal traditions should be considered by taking into account the butchery, in particular the practice of bone marrow extraction, and not only technological behaviours and types of tool kits.}, }
@article {pmid35924751, year = {2022}, author = {Roksandic, M and Radović, P and Wu, XJ and Bae, CJ}, title = {Homo bodoensis and why it matters.}, journal = {Evolutionary anthropology}, volume = {31}, number = {5}, pages = {240-244}, doi = {10.1002/evan.21954}, pmid = {35924751}, issn = {1520-6505}, mesh = {Animals ; Humans ; *Hominidae ; *Neanderthals ; }, abstract = {In our original paper, we proposed a new species, Homo bodoensis, to replace the problematical taxa Homo heidelbergensis and Homo rhodesiensis, with the goal of streamlining communication about human evolution in the Chibanian. We received two independent responses. Given their substantial overlap, we provide one combined reply. In this response: (1) we are encouraged that the primary proposal in our paper, to discontinue the use of H. heidelbergensis (as a junior synonym to Homo neanderthalensis) due to its' nomenclatural problems, is acknowledged. (2) we provide additional clarification about the rules governing taxonomic nomenclature as outlined by the International Code of Zoological Nomenclature and join the growing calls for a revision to these rules. (3) we discuss further why H. rhodesiensis should be abandoned, particularly in light of the current sensitivity to using culturally inappropriate names. We conclude that H. bodoensis is a better solution than the proposed alternatives.}, }
@article {pmid35906446, year = {2022}, author = {Andreeva, TV and Manakhov, AD and Gusev, FE and Patrikeev, AD and Golovanova, LV and Doronichev, VB and Shirobokov, IG and Rogaev, EI}, title = {Genomic analysis of a novel Neanderthal from Mezmaiskaya Cave provides insights into the genetic relationships of Middle Palaeolithic populations.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13016}, pmid = {35906446}, issn = {2045-2322}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Female ; Fossils ; Genomics ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; }, abstract = {The Mezmaiskaya cave is located on the North Caucasus near the border that divides Europe and Asia. Previously, fossil remains for two Neanderthals were reported from Mezmaiskaya Cave. A tooth from the third archaic hominin specimen (Mezmaiskaya 3) was retrieved from layer 3 in Mezmaiskaya Cave. We performed genome sequencing of Mezmaiskaya 3. Analysis of partial nuclear genome sequence revealed that it belongs to a Homo sapiens neanderthalensis female. Based on a high-coverage mitochondrial genome sequence, we demonstrated that the relationships of Mezmaiskaya 3 to Mezmaiskaya 1 and Stajnia S5000 individuals were closer than those to other Neanderthals. Our data demonstrate the close genetic connections between the early Middle Palaeolithic Neanderthals that were replaced by genetically distant later group in the same geographic areas. Based on mitochondrial DNA (mtDNA) data, we suggest that Mezmaiskaya 3 was the latest Neanderthal individual from the early Neanderthal's branches. We proposed a hierarchical nomenclature for the mtDNA haplogroups of Neanderthals. In addition, we retrieved ancestral mtDNA mutations in presumably functional sites fixed in the Neanderthal clades, and also provided the first data showing mtDNA heteroplasmy in Neanderthal specimen.}, }
@article {pmid35906286, year = {2022}, author = {Zengerling, F and Beyersdorff, D and Busch, J and Heinzelbecker, J and Pfister, D and Ruf, C and Winter, C and Albers, P and Kliesch, S and Schmidt, S}, title = {Prognostic factors in patients with clinical stage I nonseminoma-beyond lymphovascular invasion: a systematic review.}, journal = {World journal of urology}, volume = {40}, number = {12}, pages = {2879-2887}, pmid = {35906286}, issn = {1433-8726}, mesh = {Male ; Humans ; *Carcinoma, Embryonal/pathology ; Prognosis ; Neoplasm Recurrence, Local/pathology ; Neoplasm Staging ; Neoplasm Invasiveness/pathology ; *Testicular Neoplasms/pathology ; }, abstract = {OBJECTIVE: To systematically evaluate evidence on prognostic factors for tumor recurrence in clinical stage I nonseminoma patients other than lymphovascular invasion (LVI).<br><br>METHODS: We performed a systematic literature search in the biomedical databases Medline (via Ovid) and Cochrane Central Register of Controlled Trials (search period January 2010 to February 2021) for full text publications in English and German language, reporting on retro- or prospectively assessed prognostic factors for tumor recurrence in patients with stage I nonseminomatous germ cell tumors.<br><br>RESULTS: Our literature search yielded eleven studies reporting on 20 potential prognostic factors. Results are based on cohort studies of mostly moderate to low quality. Five out of eight studies found a significant association of embryonal carcinoma (EC) in the primary tumor with relapse. Among the different risk definitions of embryonal carcinoma (presence, predominance, pure), presence of EC alone seems to be sufficient for prognostification. Interesting results were found for rete testis invasion, predominant yolk sac tumor, T-stage and history of cryptorchidism, but the sparse data situation does not justify their clinical use.<br><br>CONCLUSIONS: No additional factors that meet the prognostic value of LVI, especially when determined by immunohistochemistry, could be identified through our systematic search. The presence of EC might serve as a second, subordinate prognostic factor for clinical use as the data situation is less abundant than the one of LVI. Further efforts are necessary to optimize the use of these two prognostic factors and to evaluate and validate further potential factors with promising preliminary data.}, }
@article {pmid35905187, year = {2022}, author = {Mora-Bermúdez, F and Kanis, P and Macak, D and Peters, J and Naumann, R and Xing, L and Sarov, M and Winkler, S and Oegema, CE and Haffner, C and Wimberger, P and Riesenberg, S and Maricic, T and Huttner, WB and Pääbo, S}, title = {Longer metaphase and fewer chromosome segregation errors in modern human than Neanderthal brain development.}, journal = {Science advances}, volume = {8}, number = {30}, pages = {eabn7702}, pmid = {35905187}, issn = {2375-2548}, mesh = {Animals ; Brain ; Chromosome Segregation/genetics ; *Hominidae ; Humans ; Kinesins ; Metaphase ; Mice ; *Neanderthals/genetics ; }, abstract = {Since the ancestors of modern humans separated from those of Neanderthals, around 100 amino acid substitutions spread to essentially all modern humans. The biological significance of these changes is largely unknown. Here, we examine all six such amino acid substitutions in three proteins known to have key roles in kinetochore function and chromosome segregation and to be highly expressed in the stem cells of the developing neocortex. When we introduce these modern human-specific substitutions in mice, three substitutions in two of these proteins, KIF18a and KNL1, cause metaphase prolongation and fewer chromosome segregation errors in apical progenitors of the developing neocortex. Conversely, the ancestral substitutions cause shorter metaphase length and more chromosome segregation errors in human brain organoids, similar to what we find in chimpanzee organoids. These results imply that the fidelity of chromosome segregation during neocortex development improved in modern humans after their divergence from Neanderthals.}, }
@article {pmid35874300, year = {2022}, author = {Borić, D and Cristiani, E and Hopkins, R and Schwenninger, JL and Gerometta, K and French, CAI and Mutri, G and Ćalić, J and Dimitrijević, V and Marín-Arroyo, AB and Jones, JR and Stevens, R and Masciana, A and Uno, K and Richter, KK and Antonović, D and Wehr, K and Lane, C and White, D}, title = {Neanderthals on the Lower Danube: Middle Palaeolithic evidence in the Danube Gorges of the Balkans.}, journal = {Journal of quaternary science}, volume = {37}, number = {2}, pages = {142-180}, pmid = {35874300}, issn = {0267-8179}, abstract = {The article presents evidence about the Middle Palaeolithic and Middle to Upper Palaeolithic transition interval in the karst area of the Danube Gorges in the Lower Danube Basin. We review the extant data and present new evidence from two recently investigated sites found on the Serbian side of the Danube River - Tabula Traiana and Dubočka-Kozja caves. The two sites have yielded layers dating to both the Middle and Upper Palaeolithic and have been investigated by the application of modern standards of excavation and recovery along with a suite of state-of-the-art analytical procedures. The presentation focuses on micromorphological analyses of the caves' sediments, characterisation of cryptotephra, a suite of new radiometric dates (accelerator mass spectrometry and optically stimulated luminescence) as well as proteomics (zooarchaeology by mass spectrometry) and stable isotope data in discerning patterns of human occupation of these locales over the long term.}, }
@article {pmid35874299, year = {2022}, author = {Boschin, F and Columbu, A and Spagnolo, V and Crezzini, J and Bahain, JJ and FalguèRes, C and Benazzi, S and Boscato, P and Ronchitelli, A and Moroni, A and Martini, I}, title = {Human occupation continuity in southern Italy towards the end of the Middle Palaeolithic: a palaeoenvironmental perspective from Apulia.}, journal = {Journal of quaternary science}, volume = {37}, number = {2}, pages = {204-216}, pmid = {35874299}, issn = {0267-8179}, abstract = {After the last interglacial [Marine Isotope Stage (MIS) 5e] Europe was affected by several harsh climatic oscillations. In this context southern Italy acted, like the rest of peninsular Mediterranean Europe, as a 'glacial refugium', allowing the survival of various species, and was involved in the spread of 'cold taxa' (e.g. woolly mammoth and woolly rhino) only during the coldest phases (MIS 4 and MIS 2). Both late Mousterian and early Upper Palaeolithic sites testify to a human occupation continuity in southern Italy and especially in Apulia in this time span. Here we present a focus on three key Apulian Palaeolithic sequences (Grotta di Santa Croce, Riparo L'Oscurusciuto and Grotta del Cavallo - layers F-E) jointly spanning from the late MIS 4 to the demise of Neanderthals around 43 ka. Novel chronological, sedimentological and zooarchaeological data are discussed for the first time in the light of the palaeoenvironmental information provided by recent analyses carried out on a speleothem from Pozzo Cucù cave (Bari) and the results of the magnetic susceptibility analysis from Riparo L'Oscurusciuto. This integrated reading allows a better understanding of the role played by the Apulian region as both a refugium for late Neaderthals and a suitable habitat for the early settling of modern humans.}, }
@article {pmid35865048, year = {2022}, author = {D Farhud, D and Azari, M and Mehrabi, A}, title = {The History of Corona Virus: From Neanderthals to the Present Time: A Brief Review.}, journal = {Iranian journal of public health}, volume = {51}, number = {3}, pages = {531-534}, pmid = {35865048}, issn = {2251-6093}, abstract = {Contrary to popular belief, 2019 was not the first time humans were infected by the Coronavirus. Coronavirus is one of the oldest viruses on the earth. This article discusses the history of this virus from Neanderthal time so far. We have collected a variety of articles related to coronaviruses and the extent of their interaction with humans from the first time probably appeared on earth, given that this virus is one of the ancient viruses. By examining and following the footsteps of coronaviruses in different works of literature, we found that the first homo that was infected with the coronavirus was Neanderthal. Moreover, we realized that in addition to risk factors such as age and background diseases, genetic evolution also plays an essential role in the protection of the body against coronavirus. On the other hand, this virus has evolved throughout history gradually, the same as humans. The presence of disease in humans, in any period of history, causes changes in human quality of life. Therefore, paying attention to the background of ancient diseases reveals principal information about the complexity of pathogens.}, }
@article {pmid35816093, year = {2022}, author = {Peyrégne, S and Kelso, J and Peter, BM and Pääbo, S}, title = {The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35816093}, issn = {2050-084X}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Biological Evolution ; Blacks ; Fossils ; Gene Flow ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; }, abstract = {Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show that some of the genes in which they occur may have been targets of positive selection. We also find that the two changes in the kinetochore scaffold 1 (KNL1) protein, previously believed to be specific to modern humans, were present in some Neandertals. We show that the KNL1 gene of these Neandertals shared a common ancestor with present-day Africans about 200,000 years ago due to gene flow from the ancestors (or relatives) of modern humans into Neandertals. Subsequently, some non-Africans inherited this modern human-like gene variant from Neandertals, but none inherited the ancestral gene variants. These results add to the growing evidence of early contacts between modern humans and archaic groups in Eurasia and illustrate the intricate relationships among these groups.}, }
@article {pmid35809046, year = {2022}, author = {Saha, S and Khan, N and Comi, T and Verhagen, A and Sasmal, A and Diaz, S and Yu, H and Chen, X and Akey, JM and Frank, M and Gagneux, P and Varki, A}, title = {Evolution of Human-Specific Alleles Protecting Cognitive Function of Grandmothers.}, journal = {Molecular biology and evolution}, volume = {39}, number = {8}, pages = {}, pmid = {35809046}, issn = {1537-1719}, support = {R01 GM032373/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Amino Acids ; Animals ; Cognition ; *Grandparents ; *Hominidae/genetics ; Humans ; }, abstract = {The myelomonocytic receptor CD33 (Siglec-3) inhibits innate immune reactivity by extracellular V-set domain recognition of sialic acid (Sia)-containing "self-associated molecular patterns" (SAMPs). We earlier showed that V-set domain-deficient CD33-variant allele, protective against late-onset Alzheimer's Disease (LOAD), is derived and specific to the hominin lineage. We now report multiple hominin-specific CD33 V-set domain mutations. Due to hominin-specific, fixed loss-of-function mutation in the CMAH gene, humans lack N-glycolylneuraminic acid (Neu5Gc), the preferred Sia-ligand of ancestral CD33. Mutational analysis and molecular dynamics (MD)-simulations indicate that fixed change in amino acid 21 of hominin V-set domain and conformational changes related to His45 corrected for Neu5Gc-loss by switching to N-acetylneuraminic acid (Neu5Ac)-recognition. We show that human-specific pathogens Neisseria gonorrhoeae and Group B Streptococcus selectively bind human CD33 (huCD33) as part of immune-evasive molecular mimicry of host SAMPs and that this binding is significantly impacted by amino acid 21 modification. In addition to LOAD-protective CD33 alleles, humans harbor derived, population-universal, cognition-protective variants at several other loci. Interestingly, 11 of 13 SNPs in these human genes (including CD33) are not shared by genomes of archaic hominins: Neanderthals and Denisovans. We present a plausible evolutionary scenario to compile, correlate, and comprehend existing knowledge about huCD33-evolution and suggest that grandmothering emerged in humans.}, }
@article {pmid35780191, year = {2022}, author = {Haeggström, S and Ingelman-Sundberg, M and Pääbo, S and Zeberg, H}, title = {The clinically relevant CYP2C8*3 and CYP2C9*2 haplotype is inherited from Neandertals.}, journal = {The pharmacogenomics journal}, volume = {22}, number = {4}, pages = {247-249}, pmid = {35780191}, issn = {1473-1150}, mesh = {Animals ; *Aryl Hydrocarbon Hydroxylases/genetics ; Cytochrome P-450 CYP2C8/genetics ; Cytochrome P-450 CYP2C9/genetics ; Gene Frequency ; Haplotypes/genetics ; Humans ; *Neanderthals/genetics ; }, abstract = {Genetic variation in genes encoding cytochrome P450 enzymes influences the metabolism of drugs and endogenous compounds. The locus containing the cytochrome genes CYP2C8 and CYP2C9 on chromosome 10 exhibits linkage disequilibrium between the CYP2C8*3 and CYP2C9*2 alleles, forming a haplotype of ~300 kilobases. This haplotype is associated with altered metabolism of several drugs, most notably reduced metabolism of warfarin and phenytoin, leading to toxicity at otherwise therapeutic doses. Here we show that this haplotype is inherited from Neandertals.}, }
@article {pmid35760904, year = {2022}, author = {Kerner, G and Quintana-Murci, L}, title = {The genetic and evolutionary determinants of COVID-19 susceptibility.}, journal = {European journal of human genetics : EJHG}, volume = {30}, number = {8}, pages = {915-921}, pmid = {35760904}, issn = {1476-5438}, mesh = {Biological Evolution ; *COVID-19/genetics ; Genetic Predisposition to Disease ; Humans ; Pandemics ; SARS-CoV-2 ; }, abstract = {Devastating pandemics, such as that due to COVID-19, can provide strong testimony to our knowledge of the genetic and evolutionary determinants of infectious disease susceptibility and severity. One of the most remarkable aspects of such outbreaks is the stunning interindividual variability observed in the course of infection. In recent decades, enormous progress has been made in the field of the human genetics of infectious diseases, and an increasing number of human genetic factors have been reported to explain, to a great extent, the observed variability for a large number of infectious agents. However, our understanding of the cellular, molecular, and immunological mechanisms underlying such disparities between individuals and ethnic groups, remains very limited. Here, we discuss recent findings relating to human genetic predisposition to infectious disease, from an immunological or population genetic perspective, and show how these and other innovative approaches have been applied to deciphering the genetic basis of human susceptibility to COVID-19 and the severity of this disease. From an evolutionary perspective, we show how past demographic and selection events characterizing the history of our species, including admixture with archaic humans, such as Neanderthals, facilitated modern human adaptation to the threats imposed by ancient pathogens. In the context of emerging infectious diseases, these past episodes of genetic adaptation may contribute to some of the observed population differences in the outcome of SARS-CoV-2 infection and the severity of COVID-19 illness.}, }
@article {pmid35757177, year = {2022}, author = {Theofanopoulou, C and Andirkó, A and Boeckx, C and Jarvis, ED}, title = {Oxytocin and vasotocin receptor variation and the evolution of human prosociality.}, journal = {Comprehensive psychoneuroendocrinology}, volume = {11}, number = {}, pages = {100139}, pmid = {35757177}, issn = {2666-4976}, abstract = {Modern human lifestyle strongly depends on complex social traits like empathy, tolerance and cooperation. These diverse facets of social cognition have been associated with variation in the oxytocin receptor (OTR) and its sister genes, the vasotocin/vasopressin receptors (VTR1A/AVPR1A and AVPR1B/VTR1B). Here, we compared the available genomic sequences of these receptors between modern humans, archaic humans, and 12 non-human primate species, and identified sites that show heterozygous variation in modern humans and archaic humans distinct from variation in other primates, and for which we could find association studies with clinical implications. On these sites, we performed a range of analyses (variant clustering, pathogenicity prediction, regulation, linkage disequilibrium frequency), and reviewed the literature on selection data in different modern-human populations. We found five sites with modern human specific variation, where the modern human allele is the major allele in the global population (OTR: rs1042778, rs237885, rs6770632; VTR1A: rs10877969; VTR1B: rs33985287). Among them, variation in the OTR-rs6770632 site was predicted to be the most functional. Two alleles (OTR: rs59190448 and rs237888) present only in modern humans and archaic humans were putatively under positive selection in modern humans, with rs237888 predicted to be a highly functional site. Three sites showed convergent evolution between modern humans and bonobos (OTR: rs2228485 and rs237897; VTR1A: rs1042615), with OTR-rs2228485 ranking highly in terms of functionality and reported to be under balancing selection in modern humans (Schaschl, 2015) [1]. Our findings have implications for understanding hominid prosociality, as well as the similarities between modern human and bonobo social behavior.}, }
@article {pmid35737986, year = {2022}, author = {Weasel, L}, title = {How Neanderthals Became White: The Introgression of Race into Contemporary Human Evolutionary Genetics.}, journal = {The American naturalist}, volume = {200}, number = {1}, pages = {129-139}, doi = {10.1086/720130}, pmid = {35737986}, issn = {1537-5323}, mesh = {Animals ; Genome, Human ; Genomics ; Humans ; Hybridization, Genetic ; *Neanderthals/genetics ; }, abstract = {AbstractHuman evolutionary theory has a history rife with racial biases in what might be considered its distant past that can appear glaringly obvious from our current vantage point. Despite the recognition that as a social activity science is always vulnerable to such biases (and science that attempts to uncover human origin stories all the more so), commitment to the scientific method can lead us to believe that we have improved on, overcome, or otherwise escaped these tendencies in our contemporary practices, whether through scientific contrition, changing social context, or better training and composition of research teams or as a result of advances in technologies and methodologies. This article adapts the evolutionary biology concept of introgression, which refers to the hybridization and repeated bidirectional backcross exchange of information between species, as a metaphorical frame to examine science itself and to trace the ways in which historic race biases from earlier, disowned human evolution research have been retained and selected for beneath the surface of current genomic research today. It takes as its focus the sequencing of the Neanderthal genome, first announced in 2006 and refined since, and the explosion of scientific research comparing that sequence to present-day human DNA from individuals around the world to illustrate the ways in which current research questions and findings in comparative evolutionary genomics draw on and dredge up earlier biases, albeit adapted to and disguised within contemporary social relations and power differentials.}, }
@article {pmid35729694, year = {2022}, author = {Ping, WJ and Liu, YC and Fu, QM}, title = {Exploring the evolution of archaic humans through sedimentary ancient DNA.}, journal = {Yi chuan = Hereditas}, volume = {44}, number = {5}, pages = {362-369}, doi = {10.16288/j.yczz.22-032}, pmid = {35729694}, issn = {0253-9772}, mesh = {Animals ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Genome, Human ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; }, abstract = {Recent success in the retrieval of nuclear DNA of ancient humans and animals from cave sediments paves the way for genome-wide studies of past populations directly from sediments. In three studies, nuclear genomes of different species were obtained from the sediments of multiple archeological caves and their genetic histories were revealed, including an unknown population replacement of Neanderthals from Estatuas cave in Spain, which was recovered using a new DNA capture approach. By extending sediments as a source of DNA beyond fossils, this breakthrough is of particular significance to the field of ancient human genomics, which brings about more possibilities for exploring the history of past population migration, evolution and adaptation within larger time-scales and geographical areas where no fossil remains exist. Here, we mainly review the significance of the technical advances in retrieving ancient nuclear DNA from sediments and present new insights into the genetic history of Neanderthals revealed by this technique. By combining ancient genomes retrieved from fossils and additional mitochondrial DNA extracted from sediments of archaeological sites, we may begin investigating diverse archaic populations and examine their genetic relationships, movements and replacements in detail.}, }
@article {pmid35688108, year = {2022}, author = {Pan, L and Zanolli, C and Martinón-Torres, M and Bermúdez de Castro, JM and Martín-Francés, L and Xing, S and Liu, W}, title = {Early Pleistocene hominin teeth from Gongwangling of Lantian, Central China.}, journal = {Journal of human evolution}, volume = {168}, number = {}, pages = {103212}, doi = {10.1016/j.jhevol.2022.103212}, pmid = {35688108}, issn = {1095-8606}, mesh = {Animals ; China ; Fossils ; *Hominidae/anatomy &amp; histology ; Humans ; *Neanderthals ; X-Ray Microtomography ; }, abstract = {The fossil hominin individual from Gongwangling of Lantian, Central China, represents one of the earliest members attributed to Homo erectus in East Asia. Recent paleomagnetic analyses have yielded an age of 1.63 Ma for the Gongwangling hominin. The fossils from this site are critical to characterize the morphological features of early hominins in East Asia and to understand their relationships with other earlier and later members of the genus Homo. However, most morphological details of the Gongwangling cranium were obliterated due to postmortem erosion and deformation. Here we used high-resolution microcomputed tomography and three-dimensional virtual imaging techniques to extract the teeth and reconstruct the worn/damaged areas, describe the external morphology, measure crown diameters, record nonmetric traits of the crown and root, and investigate the shape of the enamel-dentine junction using geometric morphometrics. We compared the data obtained from the six teeth of the Gongwangling hominin with African early Homo, African and Georgian Homo erectus s.l., Asian Homo erectus, Homo antecessor, pre-Neanderthals, Neanderthals, and modern humans. Our results show that the Gongwangling specimens display affinities with other specimens attributed to H. erectus s.l. The highly divergent and noncoalesced three-root system in the Gongwangling specimens is comparable to that in the Early Pleistocene members of H. erectus s.l., and differs from Middle Pleistocene representatives of the species. The enamel-dentine junction shape of the Gongwangling molars prefigures the Asian H. erectus pattern later found in East Asian Middle Pleistocene H. erectus. The morphological comparisons between East Asian Early Pleistocene (e.g., Gongwangling, Meipu, and Quyuan River Mouth) and Middle Pleistocene H. erectus (e.g., Zhoukoudian, Hexian, and Yiyuan) suggest a potential temporal trend within this species in East Asia.}, }
@article {pmid35652784, year = {2022}, author = {Marcazzan, D and Miller, CE and Ligouis, B and Duches, R and Conard, NJ and Peresani, M}, title = {Middle and Upper Paleolithic occupations of Fumane Cave (Italy): a geoarchaeological investigation of the anthropogenic features.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {100}, number = {}, pages = {}, doi = {10.4436/JASS.10002}, pmid = {35652784}, issn = {2037-0644}, abstract = {Here we present the results of a microcontextual analysis of purported combustion features recovered from Middle and Upper Paleolithic occupations at the cave site of Fumane, Italy. Our analyses, which integrate micromorphology with organic petrology, show that only a few of the features represent primary, intact hearths; some of them show evidence for various phases of anthropogenic reworking, either through trampling or sweeping and dumping. Several of the features are multi-layered and reflect a complex formation history of various activities related to combustion and site maintenance. Many appear to be the remnants of occupation horizons only partially preserved and peripherally related to combustion. Within several of the intact hearths from the Mousterian, we were able to identify variable fuel sources in different features, implying a degree of flexibility in the fuel-selection strategies of the Neanderthal occupants of Fumane. In this study we design a classification system of the anthropogenic features and also conduct a spatial analysis, through which we can infer diachronic patterns in the frequency and intensity of site occupation and the spatial distribution of activities. We note a decrease in frequency of combustion features throughout the Mousterian which continues into the Uluzzian. The features associated with the Protoaurignacian occupation, in contrast with those from the Mousterian, are multi-layered and well-defined. We argue that these trends, which correspond with other trends in artefact frequency, imply changes in the settlement dynamics of the site during the transition from the last Neanderthal occupation of the cave to the arrival of modern humans.}, }
@article {pmid35617848, year = {2022}, author = {Zubova, AV and Moiseyev, VG and Kulkov, AM and Otcherednoy, AK and Markin, SV and Kolobova, KA}, title = {Maxillary second molar from the Rozhok I Micoquian site (Azov Sea region): Another link between Eastern Europe and Siberia.}, journal = {Journal of human evolution}, volume = {168}, number = {}, pages = {103209}, doi = {10.1016/j.jhevol.2022.103209}, pmid = {35617848}, issn = {1095-8606}, mesh = {Animals ; Europe ; Europe, Eastern ; Fossils ; *Molar ; *Neanderthals ; Siberia ; }, }
@article {pmid35614148, year = {2022}, author = {Bergmann, I and Hublin, JJ and Ben-Ncer, A and Sbihi-Alaoui, FZ and Gunz, P and Freidline, SE}, title = {The relevance of late MSA mandibles on the emergence of modern morphology in Northern Africa.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8841}, pmid = {35614148}, issn = {2045-2322}, mesh = {Africa, Northern ; Animals ; Biological Evolution ; Fossils ; *Hominidae/anatomy &amp; histology ; Humans ; Mandible/anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology ; }, abstract = {North Africa is a key area for understanding hominin population movements and the expansion of our species. It is home to the earliest currently known Homo sapiens (Jebel Irhoud) and several late Middle Stone Age (MSA) fossils, notably Kébibat, Contrebandiers 1, Dar-es-Soltane II H5 and El Harhoura. Mostly referred to as "Aterian" they fill a gap in the North African fossil record between Jebel Irhoud and Iberomaurusians. We explore morphological continuity in this region by quantifying mandibular shape using 3D (semi)landmark geometric morphometric methods in a comparative framework of late Early and Middle Pleistocene hominins (n = 15), Neanderthals (n = 27) and H. sapiens (n = 145). We discovered a set of mixed features among late MSA fossils that is in line with an accretion of modern traits through time and an ongoing masticatory gracilization process. In Northern Africa, Aterians display similarities to Iberomaurusians and recent humans in the area as well as to the Tighenif and Thomas Quarry hominins, suggesting a greater time depth for regional continuity than previously assumed. The evidence we lay out for a long-term succession of hominins and humans emphasizes North Africa's role as source area of the earliest H. sapiens.}, }
@article {pmid35557944, year = {2022}, author = {Buisan, R and Moriano, J and Andirkó, A and Boeckx, C}, title = {A Brain Region-Specific Expression Profile for Genes Within Large Introgression Deserts and Under Positive Selection in Homo sapiens.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {824740}, pmid = {35557944}, issn = {2296-634X}, abstract = {Analyses of ancient DNA from extinct hominins have provided unique insights into the complex evolutionary history of Homo sapiens, intricately related to that of the Neanderthals and the Denisovans as revealed by several instances of admixture events. These analyses have also allowed the identification of introgression deserts: genomic regions in our species that are depleted of "archaic" haplotypes. The presence of genes like FOXP2 in these deserts has been taken to be suggestive of brain-related functional differences between Homo species. Here, we seek a deeper characterization of these regions and the specific expression trajectories of genes within them, taking into account signals of positive selection in our lineage. Analyzing publicly available transcriptomic data from the human brain at different developmental stages, we found that structures outside the cerebral neocortex, in particular the cerebellum, the striatum and the mediodorsal nucleus of the thalamus show the most divergent transcriptomic profiles when considering genes within large introgression deserts and under positive selection.}, }
@article {pmid35554637, year = {2022}, author = {Winter, C and Zengerling, F and Busch, J and Heinzelbecker, J and Pfister, D and Ruf, C and Lackner, J and Albers, P and Kliesch, S and Schmidt, S and Bokemeyer, C}, title = {How to classify, diagnose, treat and follow-up extragonadal germ cell tumors? A systematic review of available evidence.}, journal = {World journal of urology}, volume = {40}, number = {12}, pages = {2863-2878}, pmid = {35554637}, issn = {1433-8726}, mesh = {Male ; Humans ; Follow-Up Studies ; *Neoplasms, Germ Cell and Embryonal/therapy/drug therapy ; *Testicular Neoplasms/therapy/drug therapy ; *Seminoma/drug therapy ; *Mediastinal Neoplasms/therapy/drug therapy ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; *Neoplasms, Second Primary ; Bleomycin/therapeutic use ; }, abstract = {PURPOSE: To present the current evidence and the development of studies in recent years on the management of extragonadal germ cell tumors (EGCT).<br><br>METHODS: A systematic literature search was conducted in Medline and the Cochrane Library. Studies within the search period (January 2010 to February 2021) that addressed the classification, diagnosis, prognosis, treatment, and follow-up of extragonadal tumors were included. Risk of bias was assessed and relevant data were extracted in evidence tables.<br><br>RESULTS: The systematic search identified nine studies. Germ cell tumors (GCT) arise predominantly from within the testis, but about 5% of the tumors are primarily located extragonadal. EGCT are localized primarily mediastinal or retroperitoneal in the midline of the body. EGCT patients are classified according to the IGCCCG classification. Consecutively, all mediastinal non-seminomatous EGCT patients belong to the "poor prognosis" group. In contrast mediastinal seminoma and both retroperitoneal seminoma and non-seminoma patients seem to have a similar prognosis as patients with gonadal GCTs and metastasis at theses respective sites. The standard chemotherapy regimen for patients with a EGCT consists of 3-4 cycles (good vs intermediate prognosis) of bleomycin, etoposid, cisplatin (BEP); however, due to their very poor prognosis patients with non-seminomatous mediastinal GCT should receive a dose-intensified or high-dose chemotherapy approach upfront on an individual basis and should thus be referred to expert centers Ifosfamide may be exchanged for bleomycin in cases of additional pulmonary metastasis due to subsequently planned resections. In general patients with non-seminomatous EGCT, residual tumor resection (RTR) should be performed after chemotherapy.<br><br>CONCLUSION: In general, non-seminomatous EGCT have a poorer prognosis compared to testicular GCT, while seminomatous EGGCT seem to have a similar prognosis to patients with metastatic testicular seminoma. The current insights on EGCT are limited, since all data are mainly based on case series and studies with small patient numbers and non-comparative studies. In general, systemic treatment should be performed like in testicular metastatic GCTs but upfront dose intensification of chemotherapy should be considered for mediastinal non-seminoma patients. Thus, EGCT should be referred to interdisciplinary centers with utmost experience in the treatment of germ cell tumors.}, }
@article {pmid35546225, year = {2022}, author = {Andirkó, A and Boeckx, C}, title = {Brain region-specific effects of nearly fixed sapiens-derived alleles.}, journal = {BMC genomic data}, volume = {23}, number = {1}, pages = {36}, pmid = {35546225}, issn = {2730-6844}, mesh = {Alleles ; Animals ; Brain/metabolism ; Gene Expression Regulation ; Humans ; *Neanderthals/genetics ; }, abstract = {The availability of high-coverage genomes of our extinct relatives, the Neanderthals and Denisovans, and the emergence of large, tissue-specific databases of modern human genetic variation, offer the possibility of probing the effects of modern-derived alleles in specific tissues, such as the brain, and its specific regions. While previous research has explored the effects of introgressed variants in gene expression, the effects of Homo sapiens-specific gene expression variability are still understudied. Here we identify derived, Homo sapiens-specific high-frequency (≥90%) alleles that are associated with differential gene expression across 15 brain structures derived from the GTEx database. We show that regulation by these derived variants targets regions under positive selection more often than expected by chance, and that high-frequency derived alleles lie in functional categories related to transcriptional regulation. Our results highlight the role of these variants in gene regulation in specific regions like the cerebellum and pituitary.}, }
@article {pmid35514995, year = {2022}, author = {Mocci, S and Littera, R and Tranquilli, S and Provenzano, A and Mascia, A and Cannas, F and Lai, S and Giuressi, E and Chessa, L and Angioni, G and Campagna, M and Firinu, D and Del Zompo, M and La Nasa, G and Perra, A and Giglio, S}, title = {A Protective HLA Extended Haplotype Outweighs the Major COVID-19 Risk Factor Inherited From Neanderthals in the Sardinian Population.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {891147}, pmid = {35514995}, issn = {1664-3224}, mesh = {Animals ; *COVID-19/genetics ; Haplotypes ; Humans ; *Neanderthals/genetics ; Risk Factors ; SARS-CoV-2 ; }, abstract = {Sardinia has one of the lowest incidences of hospitalization and related mortality in Europe and yet a very high frequency of the Neanderthal risk locus variant on chromosome 3 (rs35044562), considered to be a major risk factor for a severe SARS-CoV-2 disease course. We evaluated 358 SARS-CoV-2 patients and 314 healthy Sardinian controls. One hundred and twenty patients were asymptomatic, 90 were pauci-symptomatic, 108 presented a moderate disease course and 40 were severely ill. All patients were analyzed for the Neanderthal-derived genetic variants reported as being protective (rs1156361) or causative (rs35044562) for severe illness. The β°39 C>T Thalassemia variant (rs11549407), HLA haplotypes, KIR genes, KIRs and their HLA class I ligand combinations were also investigated. Our findings revealed an increased risk for severe disease in Sardinian patients carrying the rs35044562 high risk variant [OR 5.32 (95% CI 2.53 - 12.01), p = 0.000]. Conversely, the protective effect of the HLA-A*02:01, B*18:01, DRB*03:01 three-loci extended haplotype in the Sardinian population was shown to efficiently contrast the high risk of a severe and devastating outcome of the infection predicted for carriers of the Neanderthal locus [OR 15.47 (95% CI 5.8 - 41.0), p < 0.0001]. This result suggests that the balance between risk and protective immunogenetic factors plays an important role in the evolution of COVID-19. A better understanding of these mechanisms may well turn out to be the biggest advantage in the race for the development of more efficient drugs and vaccines.}, }
@article {pmid35513387, year = {2022}, author = {Rüther, PL and Husic, IM and Bangsgaard, P and Gregersen, KM and Pantmann, P and Carvalho, M and Godinho, RM and Friedl, L and Cascalheira, J and Taurozzi, AJ and Jørkov, MLS and Benedetti, MM and Haws, J and Bicho, N and Welker, F and Cappellini, E and Olsen, JV}, title = {SPIN enables high throughput species identification of archaeological bone by proteomics.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2458}, pmid = {35513387}, issn = {2041-1723}, mesh = {Animals ; Archaeology/methods ; Chromatography, Liquid ; Mammals ; Peptides ; *Proteome ; *Proteomics/methods ; Tandem Mass Spectrometry ; }, abstract = {Species determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce "Species by Proteome INvestigation" (SPIN), a shotgun proteomics workflow for analyzing archaeological bone capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirm the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.}, }
@article {pmid35495057, year = {2022}, author = {Mora-Bermúdez, F and Huttner, WB}, title = {What Are the Human-Specific Aspects of Neocortex Development?.}, journal = {Frontiers in neuroscience}, volume = {16}, number = {}, pages = {878950}, pmid = {35495057}, issn = {1662-4548}, abstract = {When considering what makes us human, the development of the neocortex, the seat of our higher cognitive abilities, is of central importance. Throughout this complex developmental process, neocortical stem and progenitor cells (NSPCs) exert a priming role in determining neocortical tissue fate, through a series of cellular and molecular events. In this Perspective article, we address five questions of relevance for potentially human-specific aspects of NSPCs, (i) Are there human-specific NSPC subtypes? (ii) What is the functional significance of the known temporal differences in NSPC dynamics between human and other great apes? (iii) Are there functional interactions between the human-specific genes preferentially expressed in NSPCs? (iv) Do humans amplify certain metabolic pathways for NSPC proliferation? and finally (v) Have differences evolved during human evolution, notably between modern humans and Neandertals, that affect the performance of key genes operating in NSPCs? We discuss potential implications inherent to these questions, and suggest experimental approaches on how to answer them, hoping to provide incentives to further understand key issues of human cortical development.}, }
@article {pmid35484382, year = {2022}, author = {Rodríguez, J and Willmes, C and Sommer, C and Mateos, A}, title = {Sustainable human population density in Western Europe between 560.000 and 360.000 years ago.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6907}, pmid = {35484382}, issn = {2045-2322}, mesh = {Animals ; Climate Change ; Europe ; *Hominidae ; Humans ; *Neanderthals ; Population Density ; }, abstract = {The time period between 560 and 360 ka (MIS14 to MIS11) was critical for the evolution of the Neanderthal lineage and the appearance of Levallois technology in Europe. The shifts in the distribution of the human populations, driven by cyclical climate changes, are generally accepted to have played major roles in both processes. We used a dataset of palaeoclimate maps and a species distribution model to reconstruct the changes in the area of Western Europe with suitable environmental conditions for humans during 11 time intervals of the MIS14 to MIS 11 period. Eventually, the maximum sustainable human population within the suitable area during each time interval was estimated by extrapolating the relationship observed between recent hunter-gatherer population density and net primary productivity and applying it to the past. Contrary to common assumptions, our results showed the three Mediterranean Peninsulas were not the only region suitable for humans during the glacial periods. The estimated total sustainable population of Western Europe from MIS14 to MIS11 oscillated between 13,000 and 25,000 individuals. These results offer a new theoretical scenario to develop models and hypotheses to explain cultural and biological evolution during the Middle Pleistocene in Western Europe.}, }
@article {pmid35451642, year = {2022}, author = {Bruner, E and Battaglia-Mayer, A and Caminiti, R}, title = {The parietal lobe evolution and the emergence of material culture in the human genus.}, journal = {Brain structure &amp; function}, volume = {}, number = {}, pages = {}, pmid = {35451642}, issn = {1863-2661}, abstract = {Traditional and new disciplines converge in suggesting that the parietal lobe underwent a considerable expansion during human evolution. Through the study of endocasts and shape analysis, paleoneurology has shown an increased globularity of the braincase and bulging of the parietal region in modern humans, as compared to other human species, including Neandertals. Cortical complexity increased in both the superior and inferior parietal lobules. Emerging fields bridging archaeology and neuroscience supply further evidence of the involvement of the parietal cortex in human-specific behaviors related to visuospatial capacity, technological integration, self-awareness, numerosity, mathematical reasoning and language. Here, we complement these inferences on the parietal lobe evolution, with results from more classical neuroscience disciplines, such as behavioral neurophysiology, functional neuroimaging, and brain lesions; and apply these to define the neural substrates and the role of the parietal lobes in the emergence of functions at the core of material culture, such as tool-making, tool use and constructional abilities.}, }
@article {pmid35445261, year = {2022}, author = {Vallini, L and Marciani, G and Aneli, S and Bortolini, E and Benazzi, S and Pievani, T and Pagani, L}, title = {Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa.}, journal = {Genome biology and evolution}, volume = {14}, number = {4}, pages = {}, pmid = {35445261}, issn = {1759-6653}, mesh = {Africa ; Animals ; Anthropology, Cultural ; Europe ; Genetics, Population ; Humans ; *Neanderthals/genetics ; Siberia ; }, abstract = {The population dynamics that followed the Out of Africa (OoA) expansion and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macropopulations have long been debated. Shedding light on these events may, in turn, provide clues to better understand the cultural evolution in Eurasia between 50 and 35 ka. Here, we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust'Ishim, Bacho Kiro, and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 ka, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 ka, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones, whereas moving through Siberia (Yana, Mal'ta). Before these events, we also confirm Zlatý Kůň as the most basal human lineage sequenced to date OoA, potentially representing an earlier wave of expansion out of the Hub.}, }
@article {pmid35440148, year = {2022}, author = {Brand, CM and Colbran, LL and Capra, JA}, title = {Predicting Archaic Hominin Phenotypes from Genomic Data.}, journal = {Annual review of genomics and human genetics}, volume = {23}, number = {}, pages = {591-612}, doi = {10.1146/annurev-genom-111521-121903}, pmid = {35440148}, issn = {1545-293X}, support = {T32 HG009495/HG/NHGRI NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient ; Genome, Human ; Genomics ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Phenotype ; }, abstract = {Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes.}, }
@article {pmid35430882, year = {2022}, author = {Witt, KE and Villanea, F and Loughran, E and Zhang, X and Huerta-Sanchez, E}, title = {Apportioning archaic variants among modern populations.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1852}, pages = {20200411}, pmid = {35430882}, issn = {1471-2970}, support = {K99 GM143466/GM/NIGMS NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Asians/genetics ; Genetic Drift ; Genome, Human ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; }, abstract = {The apportionment of human genetic diversity within and between populations has been measured to understand human relatedness and demographic history. Likewise, the distribution of archaic ancestry in modern populations can be leveraged to better understand the interaction between our species and its archaic relatives. Resolving the interactions between modern and archaic human populations can be difficult, as archaic variants in modern populations have been shaped by genetic drift, bottlenecks and gene flow. Here, we investigate the distribution of archaic variation in Eurasian populations. We find that archaic ancestry coverage at the individual- and population-level present distinct patterns in modern human populations: South Asians have nearly twice the number of population-unique archaic alleles compared with Europeans or East Asians, indicating that these populations experienced differing demographic and archaic admixture events. We confirm previous observations that East Asian individuals have more Neanderthal ancestry than European individuals, but surprisingly, when we compare the number of single nucleotide polymorphisms with archaic alleles found across a population, Europeans have more Neanderthal ancestry than East Asians. We compare these results to simulated models and conclude that these patterns are consistent with multiple admixture events between modern humans and Neanderthals. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.}, }
@article {pmid35418680, year = {2022}, author = {Timmermann, A and Yun, KS and Raia, P and Ruan, J and Mondanaro, A and Zeller, E and Zollikofer, C and Ponce de León, M and Lemmon, D and Willeit, M and Ganopolski, A}, title = {Climate effects on archaic human habitats and species successions.}, journal = {Nature}, volume = {604}, number = {7906}, pages = {495-501}, pmid = {35418680}, issn = {1476-4687}, mesh = {Animals ; Archaeology ; Biological Evolution ; Ecosystem ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; }, abstract = {It has long been believed that climate shifts during the last 2 million years had a pivotal role in the evolution of our genus Homo[1-3]. However, given the limited number of representative palaeo-climate datasets from regions of anthropological interest, it has remained challenging to quantify this linkage. Here, we use an unprecedented transient Pleistocene coupled general circulation model simulation in combination with an extensive compilation of fossil and archaeological records to study the spatiotemporal habitat suitability for five hominin species over the past 2 million years. We show that astronomically forced changes in temperature, rainfall and terrestrial net primary production had a major impact on the observed distributions of these species. During the Early Pleistocene, hominins settled primarily in environments with weak orbital-scale climate variability. This behaviour changed substantially after the mid-Pleistocene transition, when archaic humans became global wanderers who adapted to a wide range of spatial climatic gradients. Analysis of the simulated hominin habitat overlap from approximately 300-400 thousand years ago further suggests that antiphased climate disruptions in southern Africa and Eurasia contributed to the evolutionary transformation of Homo heidelbergensis populations into Homo sapiens and Neanderthals, respectively. Our robust numerical simulations of climate-induced habitat changes provide a framework to test hypotheses on our human origin.}, }
@article {pmid35418618, year = {2022}, author = {Kubicka, AM and Balzeau, A and Kosicki, J and Nowaczewska, W and Haduch, E and Spinek, A and Piontek, J}, title = {Publisher Correction: Variation in cross-sectional indicator of femoral robusticity in Homo sapiens and Neandertals.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6226}, doi = {10.1038/s41598-022-10446-y}, pmid = {35418618}, issn = {2045-2322}, }
@article {pmid35394685, year = {2022}, author = {Pagano, AS and Smith, CM and Balzeau, A and Márquez, S and Laitman, JT}, title = {Nasopharyngeal morphology contributes to understanding the "muddle in the middle" of the Pleistocene hominin fossil record.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {305}, number = {8}, pages = {2038-2064}, doi = {10.1002/ar.24913}, pmid = {35394685}, issn = {1932-8494}, mesh = {Animals ; Biological Evolution ; Fossils ; *Hominidae/anatomy &amp; histology ; Humans ; Nasopharynx ; *Neanderthals/anatomy &amp; histology ; }, abstract = {The late archeologist Glynn Isaac first applied the term "muddle in the middle" to a poorly understood period in the Middle Pleistocene human fossil record. This study uses the nasopharyngeal boundaries as a source of traits that may inform this unclear period of human evolution. The nasopharynx lies at the nexus of several vital physiological systems, yet relatively little is known about its importance in human evolution. We analyzed a geographically diverse contemporary Homo sapiens growth series (n = 180 adults, 237 nonadults), Homo neanderthalensis (La Chapelle aux Saints 1, La Ferrassie 1, Forbes Quarry 1, Monte Circeo 1, and Saccopastore 1), mid-Pleistocene Homo (Atapuerca 5, Kabwe 1, Petralona 1, and Steinheim 1), and two Homo erectus sensu lato (KNM-ER 3733 and Sangiran 17). Methods include traditional (Analysis 1) and 3D geometric morphometric analysis (Analysis 2). H. erectus exhibited tall, narrow nasopharyngeal shape, a robust, ancestral morphology. Kabwe 1 and Petralona 1 plotted among H. sapiens in Analysis 2, exhibiting relatively shorter and vertical cartilaginous Eustachian tubes and vertical medial pterygoid plates. Atapuerca 5 and Steinheim 1 exhibited horizontal vomeral orientation similar to H. neanderthalensis, indicating greater relative soft palate length and anteroposterior nasopharynx expansion. They may exhibit synapomorphies with H. neanderthalensis, supporting the accretionary hypothesis. Species-level differences were found among H. sapiens and H. neanderthalensis, including relatively longer dilator tubae muscles and extreme facial airorhynchy among Neanderthals. Furthermore, H. neanderthalensis were autapomorphic in exhibiting horizontal pterygoid plate orientation similar to human infants, suggesting that they may have had inferiorly low placement of the torus tubarius and Eustachian tube orifice on the lateral nasopharyngeal wall in life. This study supports use of osseous nasopharyngeal boundaries both for morphological characters and understanding evolution of otitis media susceptibility in living humans.}, }
@article {pmid35353845, year = {2022}, author = {Rios-Garaizar, J and Iriarte, E and Arnold, LJ and Sánchez-Romero, L and Marín-Arroyo, AB and San Emeterio, A and Gómez-Olivencia, A and Pérez-Garrido, C and Demuro, M and Campaña, I and Bourguignon, L and Benito-Calvo, A and Iriarte, MJ and Aranburu, A and Arranz-Otaegi, A and Garate, D and Silva-Gago, M and Lahaye, C and Ortega, I}, title = {The intrusive nature of the Châtelperronian in the Iberian Peninsula.}, journal = {PloS one}, volume = {17}, number = {3}, pages = {e0265219}, pmid = {35353845}, issn = {1932-6203}, mesh = {Animals ; Europe ; Fossils ; France ; *Neanderthals ; Paris ; Technology ; }, abstract = {Multiple factors have been proposed to explain the disappearance of Neandertals between ca. 50 and 40 kyr BP. Central to these discussions has been the identification of new techno-cultural complexes that overlap with the period of Neandertal demise in Europe. One such complex is the Châtelperronian, which extends from the Paris Basin to the Northern Iberian Peninsula between 43,760-39,220 BP. In this study we present the first open-air Châtelperronian site in the Northern Iberian Peninsula, Aranbaltza II. The technological features of its stone tool assemblage show no links with previous Middle Paleolithic technology in the region, and chronological modeling reveals a gap between the latest Middle Paleolithic and the Châtelperronian in this area. We interpret this as evidence of local Neandertal extinction and replacement by other Neandertal groups coming from southern France, illustrating how local extinction episodes could have played a role in the process of disappearance of Neandertals.}, }
@article {pmid35339947, year = {2022}, author = {Roksandic, M and Radović, P and Lindal, J and Mihailović, D}, title = {Early Neanderthals in contact: The Chibanian (Middle Pleistocene) hominin dentition from Velika Balanica Cave, Southern Serbia.}, journal = {Journal of human evolution}, volume = {166}, number = {}, pages = {103175}, doi = {10.1016/j.jhevol.2022.103175}, pmid = {35339947}, issn = {1095-8606}, mesh = {Animals ; Dentition ; Fossils ; *Hominidae/anatomy &amp; histology ; Humans ; *Neanderthals ; Serbia ; }, abstract = {Neanderthals are Eurasian fossil hominins whose distinctive morphology developed in the southwestern corner of Europe and later spread throughout the continent, reaching Southwest Asia before the Late Pleistocene and spreading into Central Asia by 59-49 ka. The timing, tempo, and route of the Neanderthal movements eastward are poorly documented. The earliest probable evidence of Neanderthals in Asia comes from Karain E Cave (Anatolia, Turkey), dated to 250-200 ka. We present four Chibanian (Middle Pleistocene) hominin specimens, representing at least two individuals, from Velika Balanica Cave (Serbia): a permanent upper third molar (BH-2), a deciduous upper fourth premolar (BH-3) refitted to a poorly preserved maxillary fragment with the permanent first molar in the alveolus (BH-4), and a permanent upper central incisor (BH-5). We provide descriptions of the teeth, as well as a comparative analysis of the well-preserved M[1] (BH-4), including assessments of cusp angles, relative occlusal polygon area, relative cusp base areas, two- and three-dimensional enamel thickness, and taurodontism. Morphology of both the occlusal surface and the enamel dentine junction of the M[1] indicates that the maxillary fragment and associated dP[4] belonged to an early Neanderthal child. The heavily worn I[1] and M[3] are consistent with the Neanderthal morphology, although they are less distinct taxonomically. These Chibanian remains with provenance from layer 3a are constrained by two thermoluminescence dates: 285 ± 34 ka and 295 ± 74 ka. They represent the earliest current evidence of Neanderthal spread into the Eastern Mediterranean Area. We discuss these findings in light of recent direct evidence for cultural connections between Southwestern Asia and Southeast Europe in the Chibanian.}, }
@article {pmid35338861, year = {2022}, author = {Pop, CM and Wilson, L and Browne, CL}, title = {Evaluating landscape knowledge and lithic resource selection at the French Middle Paleolithic site of the Bau de l'Aubesier.}, journal = {Journal of human evolution}, volume = {166}, number = {}, pages = {103152}, doi = {10.1016/j.jhevol.2022.103152}, pmid = {35338861}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; *Hominidae ; }, abstract = {We report on the application of a novel approach to exploring the degree of landscape knowledge, wayfinding abilities, and the nature of decision-making processes reflected in the utilization of stone resources in the French Middle Paleolithic. Specifically, we use data from the site of the Bau de l'Aubesier to explore the reasons why a majority of the 350 raw material sources cataloged in the surrounding region appear not to have been utilized, including several located near the site and yielding high-quality lithic materials. To this end, we focus on the spatial relationships between sources as an explanatory variable, operationalized in terms of minimum travel times. Using geographic information system software and a generalized linear model of resource selection derived from the Bau assemblages, we compute source utilization probabilities from the perspective of hominins located off-site. We do so under three optimization scenarios, factoring in the intrinsic characteristics (e.g., quality) and time required to reach each source on the way to the Bau. More generally, we find that in slightly more than 50% of cases, seemingly viable sources may have been ignored simply because the minimum cost path leading back to the Bau passes through or requires only minimal deviations to reach, higher quality options. More generally, we found that throughout the entire region, a cost/benefit analysis of competing sources favors those from source areas known to have been utilized. Virtually all the available information on lithic procurement at the Bau is consistent with a model of landscape utilization premised on detailed knowledge of a very large area, an ability to accurately estimate travel times between locations, and a pragmatic strategy of stone resource exploitation based on minimizing costs (travel and search times) and maximizing utility.}, }
@article {pmid35304879, year = {2022}, author = {Kubicka, AM and Balzeau, A and Kosicki, J and Nowaczewska, W and Haduch, E and Spinek, A and Piontek, J}, title = {Variation in cross-sectional indicator of femoral robusticity in Homo sapiens and Neandertals.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4739}, pmid = {35304879}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Animals ; Bone and Bones/anatomy &amp; histology ; Femur/physiology ; Fossils ; *Hominidae/anatomy &amp; histology ; Humans ; Lower Extremity/anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology ; Tomography, X-Ray Computed ; }, abstract = {Variations in the cross-sectional properties of long bones are used to reconstruct the activity of human groups and differences in their respective habitual behaviors. Knowledge of what factors influence bone structure in Homo sapiens and Neandertals is still insufficient thus, this study investigated which biological and environmental variables influence variations in the femoral robusticity indicator of these two species. The sample consisted of 13 adult Neandertals from the Middle Paleolithic and 1959 adult individuals of H. sapiens ranging chronologically from the Upper Paleolithic to recent times. The femoral biomechanical properties were derived from the European data set, the subject literature, and new CT scans. The material was tested using a Mantel test and statistical models. In the models, the polar moment of area (J) was the dependent variable; sex, age, chronological period, type of lifestyle, percentage of the cortical area (%CA), the ratio of second moment areas of inertia about the X and Y axes (Ix/Iy), and maximum slope of the terrain were independent covariates. The Mantel tests revealed spatial autocorrelation of the femoral index in H. sapiens but not in Neandertals. A generalized additive mixed model showed that sex, %CA, Ix/Iy, chronological period, and terrain significantly influenced variation in the robusticity indicator of H. sapiens femora. A linear mixed model revealed that none of the analyzed variables correlated with the femoral robusticity indicator of Neandertals. We did not confirm that the gradual decline in the femoral robusticity indicator of H. sapiens from the Middle Paleolithic to recent times is related to the type of lifestyle; however, it may be associated with lower levels of mechanical loading during adolescence. The lack of correlation between the analysed variables and the indicator of femoral robusticity in Neandertals may suggest that they needed a different level of mechanical stimulus to produce a morphological response in the long bone than H. sapiens.}, }
@article {pmid35299091, year = {2022}, author = {Urciuoli, A and Kubat, J and Schisanowski, L and Schrenk, F and Zipfel, B and Tawane, M and Bam, L and Alba, DM and Kullmer, O}, title = {Cochlear morphology of Indonesian Homo erectus from Sangiran.}, journal = {Journal of human evolution}, volume = {165}, number = {}, pages = {103163}, doi = {10.1016/j.jhevol.2022.103163}, pmid = {35299091}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Cochlea ; *Fossils ; *Hominidae/anatomy &amp; histology ; Humans ; Indonesia ; Phylogeny ; }, abstract = {Homo erectus s.l. is key for deciphering the origin and subsequent evolution of genus Homo. However, the characterization of this species is hindered by the existence of multiple variants in both mainland and insular Asia, as a result of divergent chronogeographical evolutionary trends, genetic isolation, and interbreeding with other human species. Previous research has shown that cochlear morphology embeds taxonomic and phylogenetic information that may help infer the phylogenetic relationships among hominin species. Here we describe the cochlear morphology of two Indonesian H. erectus individuals (Sangiran 2 and 4), and compare it with a sample of australopiths, Middle to Late Pleistocene humans, and extant humans by means of linear measurements and both principal components and canonical variates analyses performed on shape ratios. Our results indicate that H. erectus displays a mosaic morphology that combines plesiomorphic (australopithlike) features (such as a chimplike round cochlear cross section and low cochlear thickness), with derived characters of later humans (a voluminous and long cochlea, possibly related to hearing abilities)-consistent with the more basal position of H. erectus. Our results also denote substantial variation between the two studied individuals, particularly in the length and radius of the first turn, as well as cross-sectional shape. Given the small size of the available sample, it is not possible to discern whether such differences merely reflect intraspecific variation among roughly coeval H. erectus individuals or whether they might result from greater age differences between them than currently considered. However, our results demonstrate that most characters found in later humans were already present in Indonesian H. erectus, with the exception of Neanderthals, which display an autapomorphic condition relative to other Homo species.}, }
@article {pmid35264715, year = {2022}, author = {Moradmand, M and Yousefi, M}, title = {Ecological niche modelling and climate change in two species groups of huntsman spider genus Eusparassus in the Western Palearctic.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4138}, pmid = {35264715}, issn = {2045-2322}, mesh = {Animals ; Biological Evolution ; Climate Change ; *Ecosystem ; Phylogeny ; *Spiders ; }, abstract = {The huntsman spiders' genus Eusparassus are apex arthropod predators in desert ecosystems of the Afrotropical and Palearctic ecoregions. The Eusparassus dufouri and E. walckenaeri clades are two distinct taxonomic, phylogenetic, and geographic units concerning morphology, molecular phylogeny, and spatial data; but little is known about their ecological niche. We applied the maximum-entropy approach and modelled ecologic niches of these two phylogenetically closely related clades. Ecological niches of the two clades were compared using identity and background tests and two different metrics, the Schooner's D and Warren's I. We also predicted the impacts of climate change on the distribution of the two clades. The results of the identity test showed that the ecological niches of the two clades were different in geographic space but were similar in environmental space. While results of the background test revealed that the ecological niches of the two clades were similar in geographic and environmental space. This indicated that "niche conservatism" had an important role over the evolutionary time of allopatric diversification. However, the normalized difference vegetation index vs. topographic heterogeneity had influenced the niches of the dufouri and walckenaeri clades, respectively. The analyses recovered that the two clades' climatically suitable habitats will increase under future climate (the year 2070). However, since the two clades are characterized by the narrow range of environmental optimum and the accordingly high limits of tolerance, they are vulnerable to climate change.}, }
@article {pmid35260774, year = {2022}, author = {Picin, A and Hajdinjak, M and Nowaczewska, W and Benazzi, S and Urbanowski, M and Marciszak, A and Fewlass, H and Bosch, MD and Socha, P and Stefaniak, K and Żarski, M and Wiśniewski, A and Hublin, JJ and Nadachowski, A and Talamo, S}, title = {Author Correction: New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4060}, doi = {10.1038/s41598-022-08141-z}, pmid = {35260774}, issn = {2045-2322}, }
@article {pmid35236981, year = {2022}, author = {Wang, FG and Yang, SX and Ge, JY and Ollé, A and Zhao, KL and Yue, JP and Rosso, DE and Douka, K and Guan, Y and Li, WY and Yang, HY and Liu, LQ and Xie, F and Guo, ZT and Zhu, RX and Deng, CL and d'Errico, F and Petraglia, M}, title = {Innovative ochre processing and tool use in China 40,000 years ago.}, journal = {Nature}, volume = {603}, number = {7900}, pages = {284-289}, pmid = {35236981}, issn = {1476-4687}, mesh = {Animals ; *Archaeology ; Bone and Bones ; China ; History, Ancient ; *Hominidae ; Humans ; Neanderthals ; *Tool Use Behavior ; }, abstract = {Homo sapiens was present in northern Asia by around 40,000 years ago, having replaced archaic populations across Eurasia after episodes of earlier population expansions and interbreeding[1-4]. Cultural adaptations of the last Neanderthals, the Denisovans and the incoming populations of H. sapiens into Asia remain unknown[1,5-7]. Here we describe Xiamabei, a well-preserved, approximately 40,000-year-old archaeological site in northern China, which includes the earliest known ochre-processing feature in east Asia, a distinctive miniaturized lithic assemblage with bladelet-like tools bearing traces of hafting, and a bone tool. The cultural assembly of traits at Xiamabei is unique for Eastern Asia and does not correspond with those found at other archaeological site assemblages inhabited by archaic populations or those generally associated with the expansion of H. sapiens, such as the Initial Upper Palaeolithic[8-10]. The record of northern Asia supports a process of technological innovations and cultural diversification emerging in a period of hominin hybridization and admixture[2,3,6,11].}, }
@article {pmid35226138, year = {2022}, author = {Pfister, D and Oechsle, K and Schmidt, S and Busch, J and Bokemeyer, C and Heidenreich, A and Heinzelbecker, J and Ruf, C and Winter, C and Zengerling, F and Kliesch, S and Albers, P and Oing, C}, title = {First-line salvage treatment options for germ cell tumor patients failing stage-adapted primary treatment : A comprehensive review compiled by the German Testicular Cancer Study Group.}, journal = {World journal of urology}, volume = {40}, number = {12}, pages = {2853-2861}, pmid = {35226138}, issn = {1433-8726}, mesh = {Male ; Humans ; *Testicular Neoplasms/pathology ; Salvage Therapy ; Cisplatin/therapeutic use ; *Hematopoietic Stem Cell Transplantation ; Retrospective Studies ; Prospective Studies ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Neoplasm Recurrence, Local/drug therapy ; Transplantation, Autologous ; *Neoplasms, Germ Cell and Embryonal/drug therapy ; }, abstract = {PURPOSE: In this review, we summarize and discuss contemporary treatment standards and possible selection criteria for decision making after failure of adjuvant or first-line cisplatin-based chemotherapy for primarily localized or metastatic germ cell tumors.<br><br>METHODS: This work is based on a systematic literature search conducted for the elaboration of the first German clinical practice guideline to identify prospective clinical trials and retrospective comparative studies published between Jan 2010 and Feb 2021. Study end points of interest were progression-free (PFS) and overall survival (OS), relapse rate (RR), and/or safety.<br><br>RESULTS: Relapses of clinical stage I (CS I) patients irrespective of prior adjuvant treatment after orchiectomy are treated stage adapted in accordance for primary metastatic patients. Surgical approaches for sole retroperitoneal relapses are investigated in ongoing clinical trials. The appropriate salvage chemotherapy for metastatic patients progressing or relapsing after first-line cisplatin-based chemotherapy is still a matter of controversy. Conventional cisplatin-based chemotherapy is the international guideline-endorsed standard of care, but based on retrospective data high-dose chemotherapy and subsequent autologous stem cell transplantation may offer a 10-15% survival benefit for all patients. Secondary complete surgical resection of all visible residual masses irrespective of size is paramount for treatment success.<br><br>CONCLUSIONS: Patients relapsing after definite treatment of locoregional disease are to be treated by stage-adapted first-line standard therapy for metastatic disease. Patients with primary advanced/metastatic disease failing one line of cisplatin-based combination chemotherapy should be referred to GCT expert centers. Dose intensity is a matter of ongoing debate, but sequential high-dose chemotherapy seems to improve patients' survival.}, }
@article {pmid35193979, year = {2022}, author = {Zeberg, H}, title = {The major genetic risk factor for severe COVID-19 is associated with protection against HIV.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {9}, pages = {}, pmid = {35193979}, issn = {1091-6490}, mesh = {COVID-19/*genetics/prevention &amp; control ; Chromosomes, Human, Pair 3/*genetics ; HIV Infections/*genetics/prevention &amp; control ; *HIV-1 ; *Haplotypes ; Humans ; Patient Acuity ; Risk Factors ; *SARS-CoV-2 ; }, abstract = {There are genetic risk factors that influence the outcome of COVID-19 [COVID-19 Host Genetics Initiative, Nature 600, 472-477 (2021)]. The major genetic risk factor for severe COIVD-19 resides on chromosome 3 and is inherited from Neandertals [H. Zeberg, S. Pääbo, Nature 587, 610-612 (2020)]. The risk-associated DNA segment modulates the expression of several chemokine receptors, among them CCR5, a coreceptor for HIV which is down-regulated in carriers of the COVID-19 risk haplotype. Here I show that carriers of the risk variant have an ∼27% lower risk of HIV infection.}, }
@article {pmid35193386, year = {2022}, author = {Cerrito, P and Nava, A and Radovčić, D and Borić, D and Cerrito, L and Basdeo, T and Ruggiero, G and Frayer, DW and Kao, AP and Bondioli, L and Mancini, L and Bromage, TG}, title = {Dental cementum virtual histology of Neanderthal teeth from Krapina (Croatia, 130-120 kyr): an informed estimate of age, sex and adult stressors.}, journal = {Journal of the Royal Society, Interface}, volume = {19}, number = {187}, pages = {20210820}, pmid = {35193386}, issn = {1742-5662}, mesh = {Adult ; Animals ; Croatia ; Dental Cementum/diagnostic imaging ; Female ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; *Tooth/diagnostic imaging ; }, abstract = {The evolution of modern human reproductive scheduling is an aspect of our life history that remains vastly uncomprehended. The present work aims to address this gap by validating a non-destructive cutting-edge methodology to infer adult life-history events on modern teeth with known life history and then applying it to fossil specimens. We use phase-contrast synchrotron X-ray microtomography to visualize the dental cementum of 21 specimens: nine contemporary humans; 10 Neanderthals from Krapina (Croatia, 130-120 kyr); one Neolithic Homo sapiens from Ajmana (Serbia); and one Mesolithic H. sapiens from Vlasac (Serbia). We were able to correctly detect and time (root mean square error = 2.1 years; R[2] = 0.98) all reproductive (menarche, parturition, menopause) and other physiologically impactful events in the modern sample. Nonetheless, we could not distinguish between the causes of the events detected. For the fossil specimens, we estimated age at death and age at occurrence of biologically significant events. Finally, we performed an exploratory analysis regarding possible sexual dimorphism in dental cementum microstructure, which allowed us to correctly infer the sex of the Neolithic specimen, for which the true value was known via DNA analysis.}, }
@article {pmid35181735, year = {2022}, author = {Lee, HK and Knabl, L and Knabl, L and Wieser, M and Mur, A and Zabernigg, A and Schumacher, J and Kapferer, S and Kaiser, N and Furth, PA and Hennighausen, L}, title = {Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {2784}, pmid = {35181735}, issn = {2045-2322}, mesh = {2',5'-Oligoadenylate Synthetase/genetics ; Adult ; Aged ; COVID-19/genetics/*immunology/virology ; Female ; *Gene Regulatory Networks ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; SARS-CoV-2/*genetics ; *Transcriptome ; Young Adult ; }, abstract = {Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. While viral infections elicit a conserved immune response, it is not known whether SARS-CoV-2 variants, which display enhanced binding to the ACE2 receptor and reduced neutralizing activity by vaccine-elicited antibodies, prompt specific genomic immune responses. To test this, we generated and investigated the transcriptomes in BCs from hospitalized patients infected with either the Alpha variant (n = 36) or with the Alpha variant that had acquired the E484K escape mutation (Alpha+E484K) (n = 13). We identified a gene module preferentially activated in patients infected with the Alpha+E484K variant and in patients infected with the Beta (n = 9) and Gamma (n = 3) variants that also carry by the E484K escape mutation. The E484K signature was enriched for genes preferentially expressed in monocytes and linked to severe viral infection. However, both cohorts had undergone similar treatments and no differences in disease severity were reported suggesting that this signature reflects a variant response and does not necessarily associate with disease outcome. Additionally, longitudinal transcriptome analyses revealed a more persistent retention of immune signatures in Alpha+E484K patients throughout the entire course of COVID-19 disease and convalescence. While the OAS1 Neanderthal mutation has been linked to a milder COVID-19 pathology, we did not identify significant immune transcriptomes differences in the 25 patients homozygous for this mutation. Our study offers insights into distinct molecular immune responses elicited by SARS-CoV-2 variants carrying the E484K escape mutation throughout the COVID-19 disease.}, }
@article {pmid35159210, year = {2022}, author = {Grigorenko, AP and Protasova, MS and Lisenkova, AA and Reshetov, DA and Andreeva, TV and Garcias, GL and Martino Roth, MDG and Papassotiropoulos, A and Rogaev, EI}, title = {Neurodevelopmental Syndrome with Intellectual Disability, Speech Impairment, and Quadrupedia Is Associated with Glutamate Receptor Delta 2 Gene Defect.}, journal = {Cells}, volume = {11}, number = {3}, pages = {}, pmid = {35159210}, issn = {2073-4409}, mesh = {Adult ; Exons ; Humans ; *Intellectual Disability/genetics ; *Neurodevelopmental Disorders/genetics ; *Receptors, Glutamate/genetics ; *Speech Disorders/genetics ; Syndrome ; }, abstract = {Bipedalism, speech, and intellect are the most prominent traits that emerged in the evolution of Homo sapiens. Here, we describe a novel genetic cause of an "involution" phenotype in four patients, who are characterized by quadrupedal locomotion, intellectual impairment, the absence of speech, small stature, and hirsutism, observed in a consanguineous Brazilian family. Using whole-genome sequencing analysis and homozygous genetic mapping, we identified genes bearing homozygous genetic variants and found a homozygous 36.2 kb deletion in the gene of glutamate receptor delta 2 (GRID2) in the patients, resulting in the lack of a coding region from the fifth to the seventh exons. The GRID2 gene is highly expressed in the cerebellum cortex from prenatal development to adulthood, specifically in Purkinje neurons. Deletion in this gene leads to the loss of the alpha chain in the extracellular amino-terminal protein domain (ATD), essential in protein folding and transport from the endoplasmic reticulum (ER) to the cell surface. Then, we studied the evolutionary trajectories of the GRID2 gene. There was no sign of strong selection of the highly conservative GRID2 gene in ancient hominids (Neanderthals and Denisovans) or modern humans; however, according to in silico tests using the Mfold tool, the GRID2 gene possibly gained human-specific mutations that increased the stability of GRID2 mRNA.}, }
@article {pmid35143674, year = {2022}, author = {Göllner, T and Larena, M and Kutanan, W and Lukas, H and Fieder, M and Schaschl, H}, title = {Unveiling the Genetic History of the Maniq, a Primary Hunter-Gatherer Society.}, journal = {Genome biology and evolution}, volume = {14}, number = {4}, pages = {}, pmid = {35143674}, issn = {1759-6653}, mesh = {Animals ; Asia, Southeastern ; *Asians ; Genetics, Population ; Humans ; *Neanderthals/genetics ; Polymorphism, Single Nucleotide ; Thailand ; }, abstract = {The Maniq of southern Thailand is one of the last remaining practicing hunter-gatherer communities in the world. However, our knowledge on their genetic origins and demographic history is still largely limited. We present here the genotype data covering ∼2.3 million single nucleotide polymorphisms of 11 unrelated Maniq individuals. Our analyses reveal the Maniq to be closely related to the Semang populations of Malaysia (Malay Negritos), who altogether carry an Andamanese-related ancestry linked to the ancient Hòabìnhian hunter-gatherers of Mainland Southeast Asia (MSEA). Moreover, the Maniq possess ∼35% East Asian-related ancestry, likely brought about by recent admixture with surrounding agriculturist communities in the region. In addition, the Maniq exhibit one of the highest levels of genetic differentiation found among living human populations, indicative of their small population size and historical practice of endogamy. Similar to other hunter-gatherer populations of MSEA, we also find the Maniq to possess low levels of Neanderthal ancestry and undetectable levels of Denisovan ancestry. Altogether, we reveal the Maniq to be a Semang group that experienced intense genetic drift and exhibits signs of ancient Hòabìnhian ancestry.}, }
@article {pmid35143314, year = {2022}, author = {Price, M}, title = {A 10,000-year head start for modern humans in Europe?.}, journal = {Science (New York, N.Y.)}, volume = {375}, number = {6581}, pages = {598-599}, doi = {10.1126/science.ada1088}, pmid = {35143314}, issn = {1095-9203}, abstract = {Tooth and tools suggest moderns and Neanderthals took turns in French cave.}, }
@article {pmid35138885, year = {2022}, author = {Slimak, L and Zanolli, C and Higham, T and Frouin, M and Schwenninger, JL and Arnold, LJ and Demuro, M and Douka, K and Mercier, N and Guérin, G and Valladas, H and Yvorra, P and Giraud, Y and Seguin-Orlando, A and Orlando, L and Lewis, JE and Muth, X and Camus, H and Vandevelde, S and Buckley, M and Mallol, C and Stringer, C and Metz, L}, title = {Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France.}, journal = {Science advances}, volume = {8}, number = {6}, pages = {eabj9496}, pmid = {35138885}, issn = {2375-2548}, abstract = {Determining the extent of overlap between modern humans and other hominins in Eurasia, such as Neanderthals and Denisovans, is fundamental to understanding the nature of their interactions and what led to the disappearance of archaic hominins. Apart from a possible sporadic pulse recorded in Greece during the Middle Pleistocene, the first settlements of modern humans in Europe have been constrained to ~45,000 to 43,000 years ago. Here, we report hominin fossils from Grotte Mandrin in France that reveal the earliest known presence of modern humans in Europe between 56,800 and 51,700 years ago. This early modern human incursion in the Rhône Valley is associated with technologies unknown in any industry of that age outside Africa or the Levant. Mandrin documents the first alternating occupation of Neanderthals and modern humans, with a modern human fossil and associated Neronian lithic industry found stratigraphically between layers containing Neanderthal remains associated with Mousterian industries.}, }
@article {pmid35125004, year = {2022}, author = {Liu, W and Athreya, S and Xing, S and Wu, X}, title = {Hominin evolution and diversity: a comparison of earlier-Middle and later-Middle Pleistocene hominin fossil variation in China.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1847}, pages = {20210040}, pmid = {35125004}, issn = {1471-2970}, mesh = {Animals ; China ; Fossils ; Gene Flow ; *Hominidae/anatomy &amp; histology ; Humans ; *Neanderthals ; }, abstract = {Historical views of Asia as an evolutionary 'backwater' are associated with the idea that Homo erectus experienced long periods of stasis and ultimately went extinct. However, recent discoveries of well-dated Middle Pleistocene hominin fossils in China have considerably challenged these ideas and provide sufficient data to propose a testable model that explains the patterning of variation in Middle Pleistocene China, and why it changed over time. A series of hominin fossil studies comparing earlier-Middle and later-Middle Pleistocene groups confirm that the expressions of certain traits shift around 300 ka. Fossils from the later Middle Pleistocene are more variable with a mix of archaic traits as well as ones that are common in Western Eurasian early Homo sapiens and Neanderthals. The period around 300 ka appears to have been a critical turning point for later-Middle Pleistocene morphological changes in China. It coincides with a phase of climatic instability in the Northern Hemisphere between Marine Isotope Stages 12 and 10 that would have led to changes in gene flow patterning, and regional population survival/extinction. This localized and testable model can be used for future explorations of hominin evolution in later Pleistocene eastern Eurasia. This article is part of the theme issue 'The impact of Chinese palaeontology on evolutionary research'.}, }
@article {pmid35075192, year = {2022}, author = {Hallinan, E and Barzilai, O and Bicho, N and Cascalheira, J and Demidenko, Y and Goder-Goldberger, M and Hovers, E and Marks, A and Oron, M and Rose, J}, title = {No direct evidence for the presence of Nubian Levallois technology and its association with Neanderthals at Shukbah Cave.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1204}, pmid = {35075192}, issn = {2045-2322}, }
@article {pmid35075170, year = {2022}, author = {Blinkhorn, J and Zanolli, C and Compton, T and Groucutt, HS and Scerri, EM and Crete, L and Stringer, C and Petraglia, MD and Blockley, S}, title = {Reply to: 'No direct evidence for the presence of Nubian Levallois technology and its association with Neanderthals at Shukbah Cave'.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1208}, pmid = {35075170}, issn = {2045-2322}, }
@article {pmid35066426, year = {2022}, author = {Mihailović, D and Kuhn, SL and Bogićević, K and Dimitrijević, V and Marín-Arroyo, AB and Marković, J and Mercier, N and Mihailović, B and Morley, MW and Radović, P and Rink, WJ and Plavšić, S and Roksandic, M}, title = {Connections between the Levant and the Balkans in the late Middle Pleistocene: Archaeological findings from Velika and Mala Balanica Caves (Serbia).}, journal = {Journal of human evolution}, volume = {163}, number = {}, pages = {103138}, doi = {10.1016/j.jhevol.2021.103138}, pmid = {35066426}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Balkan Peninsula ; Caves ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; Serbia ; }, abstract = {Major changes in the technological, economic, and social behavior of Middle Pleistocene hominins occurred at the onset of the Middle Paleolithic, 400-200 ka. However, until recently it was not possible to establish when, where, and how certain forms of Middle Paleolithic behavior appeared and spread into Southeastern Europe, mainly owing to gaps in the Paleolithic record. Here we report new results of dating, material culture, and the archaeological context of finds from the Balanica Cave Complex in Sićevo (Serbia). Two methods-thermoluminescence and electron spin resonance-were used to date the sequence. The geoarchaeological context was examined through sedimentology, micromorphology, and spatial analysis. Microfaunal remains were used to constrain the dates within an ecological zone, whereas macrofauna was analyzed for taxonomy and taphonomy to examine the source of accumulation and hominin behavior. Technological and typological features of the lithic assemblage were used to characterize lithic production at the site. Materials recovered from Layer 3 in Velika Balanica and from Layer 2 in Mala Balanica, both dated to MIS 9-7, include a distinctive set of archaeological assemblages which resemble contemporaneous Yabrudian assemblages from the Levant in important ways, and which are unlike contemporary material from the surrounding regions. In Velika Balanica, the lithic assemblages are associated with a large fireplace containing evidence of human activities similar to those from Qesem Cave (Israel). Dental remains uncovered in the same layer are consistent with Neanderthals. These findings suggest that the end of the Middle Pleistocene (before 300-240 ka) saw population movement and/or cultural transmission between Southwest Asia and the Balkans, which led eventually to a transfer of technology between Middle Eastern and European hominin populations and contributed to the shaping of Neanderthal behaviors throughout the eastern and northern Mediterranean.}, }
@article {pmid35037965, year = {2022}, author = {Busch, J and Schmidt, S and Albers, P and Heinzelbecker, J and Kliesch, S and Lackner, J and Pfister, D and Ruf, C and Winter, C and Zengerling, F and Beyersdorff, D}, title = {Can magnetic resonance imaging replace conventional computerized tomography for follow-up of patients with testicular cancer? A systematic review.}, journal = {World journal of urology}, volume = {40}, number = {12}, pages = {2843-2852}, pmid = {35037965}, issn = {1433-8726}, mesh = {Male ; Humans ; *Testicular Neoplasms/diagnostic imaging/pathology ; Prospective Studies ; Follow-Up Studies ; Magnetic Resonance Imaging ; }, abstract = {PURPOSE: Follow-up protocols for patients with testicular cancer (TC) have significantly reduced the number of cross-sectional imaging studies to reduce radiation exposure. At present, it is unclear whether magnetic resonance imaging (MRI) could replace conventional computerized tomography (CT) imaging. The objective of this study is to summarize the scientific evidence on this topic and to review guideline recommendations with regard to the use of MRI.<br><br>METHODS: A systematic literature review was performed searching Medline and Cochrane databases for prospective studies on patients with TC in the follow-up care (last search in February 2021). Additionally, guideline recommendations for TC were screened. Data extraction and quality assessment of included studies were performed and used for a descriptive presentation of results.<br><br>RESULTS: A total of four studies including two ongoing trials were identified. Overall, the scientific evidence of prospective comparative studies is based on 102 patients. Data suggest that abdominal imaging with MRI can replace conventional CT for detection of lymph node metastasis of the retroperitoneum to spare radiation exposure and contrast media application. However, experienced radiologists are needed. Clinical guidelines are aware of the risk of diagnosis-induced secondary malignancy due to CT imaging and some have adapted their recommendations accordingly. Results of the two ongoing trials on 738 patients are expected soon to provide more reliable results on this topic.<br><br>CONCLUSIONS: There is growing evidence that abdominopelvic MRI imaging can replace CT imaging during follow-up of patients with TC in order to reduce radiation exposure and diagnosis-induced secondary malignancy.}, }
@article {pmid35027740, year = {2022}, author = {Huffman, JE and Butler-Laporte, G and Khan, A and Pairo-Castineira, E and Drivas, TG and Peloso, GM and Nakanishi, T and ,  and Ganna, A and Verma, A and Baillie, JK and Kiryluk, K and Richards, JB and Zeberg, H}, title = {Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19.}, journal = {Nature genetics}, volume = {54}, number = {2}, pages = {125-127}, pmid = {35027740}, issn = {1546-1718}, support = {UL1 TR001878/TR/NCATS NIH HHS/United States ; K25 DK128563/DK/NIDDK NIH HHS/United States ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; UL1 TR001873/TR/NCATS NIH HHS/United States ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; }, mesh = {2',5'-Oligoadenylate Synthetase/*genetics ; Blacks/genetics ; COVID-19/enzymology/*genetics/*pathology ; *Genetic Predisposition to Disease ; Humans ; Linkage Disequilibrium/genetics ; *Physical Chromosome Mapping ; RNA Splicing/*genetics ; Risk Factors ; *Severity of Illness Index ; Whites/genetics ; }, abstract = {The OAS1/2/3 cluster has been identified as a risk locus for severe COVID-19 among individuals of European ancestry, with a protective haplotype of approximately 75 kilobases (kb) derived from Neanderthals in the chromosomal region 12q24.13. This haplotype contains a splice variant of OAS1, which occurs in people of African ancestry independently of gene flow from Neanderthals. Using trans-ancestry fine-mapping approaches in 20,779 hospitalized cases, we demonstrate that this splice variant is likely to be the SNP responsible for the association at this locus, thus strongly implicating OAS1 as an effector gene influencing COVID-19 severity.}, }
@article {pmid35026677, year = {2022}, author = {Wu, XJ and Bae, CJ and Friess, M and Xing, S and Athreya, S and Liu, W}, title = {Evolution of cranial capacity revisited: A view from the late Middle Pleistocene cranium from Xujiayao, China.}, journal = {Journal of human evolution}, volume = {163}, number = {}, pages = {103119}, doi = {10.1016/j.jhevol.2021.103119}, pmid = {35026677}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; China ; Fossils ; *Hominidae/anatomy &amp; histology ; Humans ; *Neanderthals/anatomy &amp; histology ; Skull/anatomy &amp; histology ; Temporal Bone/anatomy &amp; histology ; }, abstract = {The Late Middle Pleistocene hominin fossils from the Xujiayao site in northern China have been closely studied in light of their morphological variability. However, all previous studies have focused on separated cranial fragments. Here, we report the first reconstruction of a fairly complete posterior cranium, Xujiayao 6 (XJY 6), confidently dated to ∼200-160 ka, which facilitated an assessment of its overall cranial size. XJY 6 was reconstructed from three of the original fragments-the PA1486 (No.7/XJY 6a) occipital bone, PA1490 (No.10/XJY 6b) right parietal bone, and PA1498 (No.17/XJY 15) left temporal bone-which originated from the same young adult individual. The XJY 6 endocranial capacity, estimated by measuring endocranial volume, was estimated using multiple regression formulae derived from ectocranial and endocranial measurements on select samples of Pleistocene hominins and recent modern humans. The results indicate that the larger pooled sample of both Pleistocene and recent modern humans was more robust for the endocranial capacity estimate. Based on the pooled sample using the ectocranial and endocranial measurements, we conservatively estimate the XJY 6 endocranial volume to be ∼1700 cm[3] with a 95% confidence interval of 1555-1781 cm[3]. This is close to Xuchang 1, which dates to 125-105 ka and whose endocranial volume is ∼1800 cm[3]. Thus, XJY 6 provides the earliest evidence of a brain size that falls in the upper range of Neanderthals and modern Homo sapiens. XJY 6, together with Xuchang 1, Homo floresiensis, Homo luzonensis, and Homo naledi, challenge the general pattern that brain size gradually increases over geological time. This study also finds that hominin brain size expansion occurred at different rates across time and space.}, }
@article {pmid35013414, year = {2022}, author = {Koch, TJ and Schmidt, P}, title = {A new method for birch tar making with materials available in the Stone Age.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {413}, pmid = {35013414}, issn = {2045-2322}, abstract = {The use of birch tar can be traced back to the European Middle Palaeolithic and is relevant for our understanding of the technical skills and cognitive abilities of Neanderthals. Due to the lack of archaeological evidence, it remains unknown what techniques were used for birch tar making. Efficiency was recently used as a proxy to determine the method most likely used in the Middle Palaeolithic. Todtenhaupt et al. have proposed a technique employing a groove-like structure that is comparable with the recently presented condensation method. The groove method resulted in higher tar yields compared to other experimental aceramic production processes. However, the implications for Palaeolithic tar making remain unclear because some of the materials used in the experiment were not available then (polished granite slabs). To approach this problem, we replicated the groove with river cobbles and, in a second experiment with flint fragments, to evaluate whether similar results can be obtained. We were successful in producing birch tar in multiple runs with the cobble- and flint-grooves, which, in addition, proved to be more efficient than the condensation method in terms of tar yield per bark input. Our experimental study provides an additional possibility to make prehistoric birch tar.}, }
@article {pmid34998272, year = {2022}, author = {Zanolli, C and Kaifu, Y and Pan, L and Xing, S and Mijares, AS and Kullmer, O and Schrenk, F and Corny, J and Dizon, E and Robles, E and Détroit, F}, title = {Further analyses of the structural organization of Homo luzonensis teeth: Evolutionary implications.}, journal = {Journal of human evolution}, volume = {163}, number = {}, pages = {103124}, doi = {10.1016/j.jhevol.2021.103124}, pmid = {34998272}, issn = {1095-8606}, mesh = {Animals ; Bicuspid ; Biological Evolution ; *Fossils ; *Hominidae/anatomy &amp; histology ; Humans ; *Molar, Third ; Philippines ; Phylogeny ; }, abstract = {The species Homo luzonensis has recently been described based on a set of dental and postcranial elements found at Callao Cave (Northern Luzon, Philippines) and dated to at least 50-67 ka. Seven postcanine maxillary teeth are attributed to this taxon, five of them belonging to the same individual (CCH6) and representing the holotype of H. luzonensis, whereas the isolated upper premolar CCH8 and the upper third molar CCH9 are paratypes of the species. The teeth are characterized by their small dimensions associated with primitive features, as also found in Homo floresiensis, another hominin having evolved in an insular environment of Southeast Asia. Postcranial bones of the hands and feet of H. luzonensis and H. floresiensis show Homo habilis-like or australopith-like features, whereas cranial and dental morphology are more consistent with the Asian Homo erectus morphology. Due to this mosaic morphology, the origin and phylogenetic relationships of both H. luzonensis and H. floresiensis are still debated. To test the hypotheses that H. luzonensis derives from H. erectus or from an earlier small-brained hominin, we analyzed the µCT scans of the teeth. We investigated both external and internal tooth structure using morphometric methods including: crown outline shape, tooth crown tissue proportions, enamel-dentine junction shape, and pulp morphology. Homo luzonensis external crown morphology aligns more with H. erectus than with H. habilis/H. rudolfensis. The internal structural organization of H. luzonensis teeth exhibits more affinities with that of H. erectus and H. floresiensis than with Neanderthals and modern humans. Our results suggest that both H. floresiensis and H. luzonensis likely evolved from some H. erectus groups that dispersed in the various islands of this region and became isolated until endemic speciation events occurred at least twice during the Pleistocene in insular environments.}, }
@article {pmid34989121, year = {2022}, author = {Balzeau, A and Pagano, A}, title = {The cranial base and related internal anatomical features in Homo neanderthalensis and Homo sapiens.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {305}, number = {8}, pages = {2030-2037}, doi = {10.1002/ar.24854}, pmid = {34989121}, issn = {1932-8494}, mesh = {Animals ; *Eustachian Tube/anatomy &amp; histology ; Fossils ; *Hominidae/anatomy &amp; histology ; Humans ; *Neanderthals/anatomy &amp; histology ; Palatal Muscles ; Skull Base/anatomy &amp; histology/diagnostic imaging ; }, abstract = {The cranial anatomy of Homo neanderthalensis and Homo sapiens is well documented in the paleoanthropological and medical literature. However, there are few high-quality visual guides of their comparative morphology. We give here a detailed description of the anatomy of two important fossil specimens, La Chapelle-aux-Saints 1 and abri Pataud 1, based on high-resolution imaging data with each specimen representing the respective morphologies of H. neanderthalensis and H. sapiens. We describe the comparative morphology of external, endocranial, and internal characteristics of the cranium, with a focus on the petrous and tympanic portions of the temporal bone. This descriptive approach shows differences between our specimens, including in positions of cerebral components relative to cranial structures and patterns of dural sinus drainage. Numerous external and internal differences in the shape of the petrous temporal are also described, including its articulation with the tympanic bone and the orientation of the petrotympanic crest. The presence of a large protuberance between the osseous Eustachian tube orifice and carotid foramen in H. neanderthalensis suggests that the levator veli palatini muscle took origin more laterally than the dilator tubae arm of the tensor veli palatini muscle, a feature shared with H. sapiens. The overall pattern that emerges is one in which two species have undergone large-scale evolutionary changes in a functionally critical region. Such differences necessitate high-quality visualization and consideration of both internal and external morphology.}, }
@article {pmid34985944, year = {2022}, author = {Coppo, L and Mishra, P and Siefert, N and Holmgren, A and Pääbo, S and Zeberg, H}, title = {A substitution in the glutathione reductase lowers electron leakage and inflammation in modern humans.}, journal = {Science advances}, volume = {8}, number = {1}, pages = {eabm1148}, pmid = {34985944}, issn = {2375-2548}, abstract = {Glutathione reductase is a critical enzyme for preventing oxidative stress and maintaining a reduced intracellular environment. Almost all present-day humans carry an amino acid substitution (S232G) in this enzyme relative to apes and Neanderthals. We express the modern human and the ancestral enzymes and show that whereas the activity and stability are unaffected by the amino acid substitution, the ancestral enzyme produces more reactive oxygen species and increases cellular levels of transcripts encoding cytokines. We furthermore show that the ancestral enzyme has been reintroduced into the modern human gene pool by gene flow from Neanderthals and is associated with multiple traits in present-day people, including increased susceptibility for inflammatory-associated disorders and vascular disease.}, }
@article {pmid34969841, year = {2022}, author = {Massilani, D and Morley, MW and Mentzer, SM and Aldeias, V and Vernot, B and Miller, C and Stahlschmidt, M and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Conard, NJ and Wurz, S and Henshilwood, CS and Vasquez, J and Essel, E and Nagel, S and Richter, J and Nickel, B and Roberts, RG and Pääbo, S and Slon, V and Goldberg, P and Meyer, M}, title = {Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {1}, pages = {}, pmid = {34969841}, issn = {1091-6490}, mesh = {Animals ; *Caves ; *DNA, Ancient ; *Fossils ; Hominidae/*genetics ; Neanderthals/*genetics ; }, abstract = {Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.}, }
@article {pmid34943532, year = {2021}, author = {Durand, S and Dufour, J and Rosas, A and Becce, F and Orr, C}, title = {Three-Dimensional Comparative Study of Human Bipartite Scaphoids and the Os Centrale of the Wrist in Neandertals and Non-Human Anthropoid Primates.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {34943532}, issn = {2075-4418}, abstract = {In humans, bipartite scaphoid still does not differentiate clearly from traumatic non-union of the scaphoid. To aid diagnosis, we sought to analyze the main geometrical similarities among bipartite scaphoids from primate species with fused and unfused scaphoid centrales. Four human embryos, four cases of adult humans with bipartite scaphoid, twelve adult specimens of other extant anthropoid primates, and two Neandertal scaphoid specimens were included in this study. Three-dimensional polygon models of the scaphoid and os centrale were generated from CT scan, micro-CT scan, or histological sections. A 3D comparative study of the morphological and morphometrical parameters was performed using the MSC Patran software. The os centrale was smaller than the scaphoid in all specimens and its shape was elongated in the anteroposterior scaphoid direction. The position of the os centrale centroid compared to the scaphoid using direction vectors had a strong orientation along the proximodistal axis in all species. The main morphological feature of bipartite scaphoid was the continuity of the scaphoid from its proximal pole to its tubercule along the anteroposterior axis. In all specimens, if the os centrale was removed, the scaphoid still appeared normal and whole. The bipartite scaphoid in adult humans shares geometrical analogies with monkeys and orangutans, human embryos, and Neandertals. Morphological and morphometrical features identified in this study are useful to differentiate bipartite scaphoid from scaphoid pseudarthrosis. All other criteria suggested in the past lead to misdiagnosis.}, }
@article {pmid34937535, year = {2021}, author = {Zhur, KV and Trifonov, VA and Prokhortchouk, EB}, title = {Progress and Prospects in Epigenetic Studies of Ancient DNA.}, journal = {Biochemistry. Biokhimiia}, volume = {86}, number = {12}, pages = {1563-1571}, doi = {10.1134/S0006297921120051}, pmid = {34937535}, issn = {1608-3040}, mesh = {Animals ; *DNA Methylation ; *DNA, Ancient ; *Epigenesis, Genetic ; Epigenomics/trends ; *Evolution, Molecular ; Human Migration ; Humans ; Neanderthals/*genetics ; }, abstract = {Development of technologies for high-throughput whole-genome sequencing and improvement of sample preparation techniques made it possible to study ancient DNA (aDNA) from archaeological samples over a million year old. The studies of aDNA have shed light on the history of human migration, replacement of populations, interbreeding of Cro-Magnons with Neanderthals and Denisovans, evolution of human pathogens, etc. Equally important is the possibility to investigate epigenetic modifications of ancient genomes, which has allowed to obtain previously inaccessible information on gene expression, nucleosome positioning, and DNA methylation. Analysis of methylation status of certain genomic sites can predict an individual's age at death and reconstruct some phenotypic features, as it was done for the Denisovan genome, and even to elucidate unfavorable environmental factors that had affected this archaic individual. In this review, we discuss current progress in epigenetic studies of aDNA, including methodological approaches and promising research directions in this field.}, }
@article {pmid34923240, year = {2022}, author = {Hardy, K and Bocherens, H and Miller, JB and Copeland, L}, title = {Reconstructing Neanderthal diet: The case for carbohydrates.}, journal = {Journal of human evolution}, volume = {162}, number = {}, pages = {103105}, doi = {10.1016/j.jhevol.2021.103105}, pmid = {34923240}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Carbohydrates ; Diet ; *Hominidae ; Humans ; *Neanderthals/physiology ; }, abstract = {Evidence for plants rarely survives on Paleolithic sites, while animal bones and biomolecular analyses suggest animal produce was important to hominin populations, leading to the perspective that Neanderthals had a very-high-protein diet. But although individual and short-term survival is possible on a relatively low-carbohydrate diet, populations are unlikely to have thrived and reproduced without plants and the carbohydrates they provide. Today, nutritional guidelines recommend that around half the diet should be carbohydrate, while low intake is considered to compromise physical performance and successful reproduction. This is likely to have been the same for Paleolithic populations, highlighting an anomaly in that the basic physiological recommendations do not match the extensive archaeological evidence. Neanderthals had large, energy-expensive brains and led physically active lifestyles, suggesting that for optimal health they would have required high amounts of carbohydrates. To address this anomaly, we begin by outlining the essential role of carbohydrates in the human reproduction cycle and the brain and the effects on physical performance. We then evaluate the evidence for resource availability and the archaeological evidence for Neanderthal diet and investigate three ways that the anomaly between the archaeological evidence and the hypothetical dietary requirements might be explained. First, Neanderthals may have had an as yet unidentified genetic adaptation to an alternative physiological method to spare blood glucose and glycogen reserves for essential purposes. Second, they may have existed on a less-than-optimum diet and survived rather than thrived. Third, the methods used in dietary reconstruction could mask a complex combination of dietary plant and animal proportions. We end by proposing that analyses of Paleolithic diet and subsistence strategies need to be grounded in the minimum recommendations throughout the life course and that this provides a context for interpretation of the archaeological evidence from the behavioral and environmental perspectives.}, }
@article {pmid34919805, year = {2022}, author = {Natri, HM and Hudjashov, G and Jacobs, G and Kusuma, P and Saag, L and Darusallam, CC and Metspalu, M and Sudoyo, H and Cox, MP and Gallego Romero, I and Banovich, NE}, title = {Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries.}, journal = {American journal of human genetics}, volume = {109}, number = {1}, pages = {50-65}, pmid = {34919805}, issn = {1537-6605}, mesh = {Computational Biology/methods ; DNA Methylation ; Databases, Genetic ; *Gene Expression Regulation ; *Genetics, Population ; *Genome, Human ; Genome-Wide Association Study ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Indonesia ; Male ; Models, Genetic ; Molecular Sequence Annotation ; Multifactorial Inheritance ; *Quantitative Trait Loci ; Quantitative Trait, Heritable ; Selection, Genetic ; Whole Genome Sequencing ; }, abstract = {Lack of diversity in human genomics limits our understanding of the genetic underpinnings of complex traits, hinders precision medicine, and contributes to health disparities. To map genetic effects on gene regulation in the underrepresented Indonesian population, we have integrated genotype, gene expression, and CpG methylation data from 115 participants across three island populations that capture the major sources of genomic diversity in the region. In a comparison with European datasets, we identify eQTLs shared between Indonesia and Europe as well as population-specific eQTLs that exhibit differences in allele frequencies and/or overall expression levels between populations. By combining local ancestry and archaic introgression inference with eQTLs and methylQTLs, we identify regulatory loci driven by modern Papuan ancestry as well as introgressed Denisovan and Neanderthal variation. GWAS colocalization connects QTLs detected here to hematological traits, and further comparison with European datasets reflects the poor overall transferability of GWAS statistics across diverse populations. Our findings illustrate how population-specific genetic architecture, local ancestry, and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations and highlight the need for performing association studies on non-European populations.}, }
@article {pmid34915249, year = {2022}, author = {Williams, MJ}, title = {The term "psychosis" is archaic.}, journal = {Schizophrenia research}, volume = {240}, number = {}, pages = {31}, doi = {10.1016/j.schres.2021.12.003}, pmid = {34915249}, issn = {1573-2509}, mesh = {Animals ; *Hominidae ; Humans ; *Neanderthals ; }, }
@article {pmid34914745, year = {2021}, author = {Hayakawa, T and Terahara, M and Fujito, NT and Matsunaga, T and Teshima, KM and Hane, M and Kitajima, K and Sato, C and Takahata, N and Satta, Y}, title = {Lower promoter activity of the ST8SIA2 gene has been favored in evolving human collective brains.}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0259897}, pmid = {34914745}, issn = {1932-6203}, mesh = {Animals ; Brain/*enzymology ; Databases, Genetic ; Genetic Loci ; Haplotypes ; Humans ; Neanderthals/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Promoter Regions, Genetic ; Schizophrenia/genetics/pathology ; Sialyltransferases/classification/*genetics ; }, abstract = {ST8SIA2 is an important molecule regulating expression of the phenotype involved in schizophrenia. Lowered promoter activity of the ST8SIA2 gene is considered to be protective against schizophrenia by conferring tolerance to psychosocial stress. Here, we examined the promoter-type composition of anatomically modern humans (AMHs) and archaic humans (AHs; Neanderthals and Denisovans), and compared the promoter activity at the population level (population promoter activity; PPA) between them. In AMHs, the TCT-type, showing the second lowest promoter activity, was most prevalent in the ancestral population of non-Africans. However, the detection of only the CGT-type from AH samples and recombination tracts in AH sequences showed that the CGT- and TGT-types, exhibiting the two highest promoter activities, were common in AH populations. Furthermore, interspecies gene flow occurred into AMHs from AHs and into Denisovans from Neanderthals, influencing promoter-type compositions independently in both AMHs and AHs. The difference of promoter-type composition makes PPA unique in each population. East and Southeast Asian populations show the lowest PPA. This results from the selective increase of the CGC-type, showing the lowest promoter activity, in these populations. Every non-African population shows significantly lower PPA than African populations, resulting from the TCT-type having the highest prevalence in the ancestral population of non-Africans. In addition, PPA reduction is also found among subpopulations within Africa via a slight increase of the TCT-type. These findings indicate a trend toward lower PPA in the spread of AMHs, interpreted as a continuous adaptation to psychosocial stress arising in migration. This trend is considered as genetic tuning for the evolution of collective brains. The inferred promoter-type composition of AHs differed markedly from that of AMHs, resulting in higher PPA in AHs than in AMHs. This suggests that the trend toward lower PPA is a unique feature in AMH spread.}, }
@article {pmid34913347, year = {2021}, author = {Hubacek, JA}, title = {Effects of selected inherited factors on susceptibility to SARS-CoV-2 infection and COVID-19 progression.}, journal = {Physiological research}, volume = {70}, number = {S2}, pages = {S125-S134}, pmid = {34913347}, issn = {1802-9973}, mesh = {ABO Blood-Group System/genetics ; Angiotensin-Converting Enzyme 2/genetics ; Animals ; Apolipoproteins E/genetics ; COVID-19/*genetics/virology ; Disease Progression ; Genetic Predisposition to Disease ; Heredity ; Host-Pathogen Interactions ; Humans ; Phenotype ; *Polymorphism, Genetic ; Risk Assessment ; Risk Factors ; SARS-CoV-2/*pathogenicity ; Serine Endopeptidases/genetics ; }, abstract = {Genetic predispositions may influence geographical and interethnic differences in COVID-19 prevalence and mortality in affected populations. Of the many genes implicated in COVID-19 progression, a substantial number have no direct functional link on virus transfer/viability or on the host immune system. To address this knowledge deficit, a large number of in silico studies have recently been published. However, the results of these studies often contradict the findings of studies involving real patients. For example, the ACE2 has been shown to play an important role in regulating coronavirus entry into cells, but none of its variations have been directly associated with COVID-19 susceptibility or severity. Consistently was reported that increased risk of COVID-19 is associated with blood group A and with the APOE4 allele. Among other genes with potential impacts are the genes for CCR5, IL-10, CD14, TMPRSS2 and angiotensin-converting enzyme. Variants within the protein-coding genes OAS1 and LZTFL1 (transferred to the human genome from Neanderthals) are understood to be among the strongest predictors of disease severity. The intensive research efforts have helped to identify the genes and polymorphisms that contribute to SARS-CoV-2 infection and COVID-19 severity.}, }
@article {pmid34910514, year = {2021}, author = {Roebroeks, W and MacDonald, K and Scherjon, F and Bakels, C and Kindler, L and Nikulina, A and Pop, E and Gaudzinski-Windheuser, S}, title = {Landscape modification by Last Interglacial Neanderthals.}, journal = {Science advances}, volume = {7}, number = {51}, pages = {eabj5567}, pmid = {34910514}, issn = {2375-2548}, abstract = {Little is known about the antiquity, nature, and scale of Pleistocene hunter-gatherer impact on their ecosystems, despite the importance for studies of conservation and human evolution. Such impact is likely to be limited, mainly because of low population densities, and challenging to detect and interpret in terms of cause-effect dynamics. We present high-resolution paleoenvironmental and archaeological data from the Last Interglacial locality of Neumark-Nord (Germany). Among the factors that shaped vegetation structure and succession in this lake landscape, we identify a distinct ecological footprint of hominin activities, including fire use. We compare these data with evidence from archaeological and baseline sites from the same region. At Neumark-Nord, notably open vegetation coincides with a virtually continuous c. 2000-year-long hominin presence, and the comparative data strongly suggest that hominins were a contributing factor. With an age of c. 125,000 years, Neumark-Nord provides an early example of a hominin role in vegetation transformation.}, }
@article {pmid34897365, year = {2022}, author = {Decaup, PH and Couture, C and Colin, M and Garot, E}, title = {Prevalence of taurodontism: meta-analysis in recent humans and evolutionary perspectives.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {73}, number = {1}, pages = {1-11}, doi = {10.1127/homo/2021/1447}, pmid = {34897365}, issn = {1618-1301}, mesh = {Animals ; Humans ; *Neanderthals ; Prevalence ; Cross-Sectional Studies ; *Tooth Abnormalities ; *Hominidae ; }, abstract = {Taurodontism is a continuous anatomical variation of permanent and primary posterior teeth represented by an enlargement of the pulp cavity. A high prevalence of the trait is reported in Homo neanderthalensis remains. Exploring and refining epidemiology of taurodontism in actual populations could strengthen the hypothesis of a selective advantage for a high attrition diet (as heavy tooth wear in Homo sapiens evolution changed little until recently) or favour pleiotropic or genetic drift effects to explain the high frequency of the trait in Neandertal remains. Prevalence ranges between 0.1% and 48% in the literature. The aim of the present study is to assess the prevalence of taurodontism in recent populations by means of meta-analysis, that is, is the prevalence of taurodontism lower or higher in modern human living populations, where the selective advantages of high attrition diet are still expected? From 90 potentially eligible studies, 15 were included in the meta-analysis. Only cross-sectional studies were reported, and 14,771 participants were included. The meta-analyses were performed with a random model, calculating a weighted-mean prevalence of 11.8%. Gender was found to be unrelated to the prevalence of taurodontism (OR = 0.84 (95% CI 0.67-1.05), p > 0.05). Taurodontism occurs in approximately 11.8% of the living population. This result questions the status of taurodontism as a "typical trait" in Homo neanderthalensis and allows a possible common evolutionary mechanism in Homo sapiens and Homo neanderthalensis for the trait. Further studies should include more accurate and standardized methods to assess the condition.}, }
@article {pmid34866354, year = {2021}, author = {Bermúdez de Castro, JM and Martínez de Pinillos, M and Martín-Francés, L and Modesto-Mata, M and García-Campos, C and Arsuaga, JL and Martinón-Torres, M}, title = {Dental remains of the Middle Pleistocene hominins from the Sima de los Huesos site (Sierra de Atapuerca, Spain): Maxillary dentition.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.24841}, pmid = {34866354}, issn = {1932-8494}, abstract = {The Middle Pleistocene site of the Sima de los Huesos (Sierra de Atapuerca, northern Spain) has yielded a considerable number of human fossils during the period 1984-2020. Among them, up to 253 maxillary teeth have been recovered. In this article, we present the description of the eight dental classes of the maxilla following the Arizona State University Dental Anthropology System classification. In addition, we present the mean mesiodistal and buccolingual diameters of these teeth compared to those of Neanderthals and a modern human sample. The morphology of both the anterior and posterior teeth suggests a close relationship of the Sima de los Huesos hominins with the populations of the second half of the Middle Pleistocene of Europe and the Near East, as well as with the so-called classic Neanderthals of Europe. Features with a recognizable taxonomic signal allow grouping the Sima de los Huesos hominins with different paleodemes into a Neanderthal clade. The dental evidence of the Sima de los Huesos hominins is key to suggest a complex model for the settlement of Europe during the Middle Pleistocene. During this period, different migrations of human groups probably coming from Southwest Asia, replacements, prolonged isolations, as well as hybridization and introgression processes would have contributed to the diversity of hominins in Europe.}, }
@article {pmid34855484, year = {2021}, author = {Marom, A and Rak, Y}, title = {Comment on "A Middle Pleistocene Homo from Nesher Ramla, Israel".}, journal = {Science (New York, N.Y.)}, volume = {374}, number = {6572}, pages = {eabl4336}, doi = {10.1126/science.abl4336}, pmid = {34855484}, issn = {1095-9203}, mesh = {Animals ; *Fossils ; Hominidae/classification ; Israel ; Mandible/anatomy &amp; histology ; Neanderthals/*classification ; }, abstract = {Hershkovitz et al. (Reports, 25 June 2021, p. 1424) conclude that the Nesher Ramla (NR) fossils represent a distinctive Homo paleodeme that played a role as a source population for Neanderthals. However, the highly diagnostic features of the Neanderthal mandible—clearly displayed by the NR fossils—are largely overlooked. Our analyses indicate that the NR fossils represent simply a Neanderthal.}, }
@article {pmid34855476, year = {2021}, author = {May, H and Sarig, R and Pokhojaev, A and Fornai, C and Martinón-Torres, M and Bermúdez de Castro, JM and Weber, GW and Zaidner, Y and Hershkovitz, I}, title = {Response to Comment on "A Middle Pleistocene Homo from Nesher Ramla, Israel".}, journal = {Science (New York, N.Y.)}, volume = {374}, number = {6572}, pages = {eabl5789}, doi = {10.1126/science.abl5789}, pmid = {34855476}, issn = {1095-9203}, mesh = {*Fossils ; Israel ; }, abstract = {Marom and Rak claim, on the basis of a few mandibular features, that the Nesher Ramla (NR) Homo is a Neanderthal. Their comments lack substance and contribute little to the debate surrounding the evolution of Middle Pleistocene Homo. Limitations and preconceptions in their study prevented them from achieving resolution beyond a dichotomous interpretation of the NR as either a Neanderthal or a modern human.}, }
@article {pmid34851548, year = {2021}, author = {Bermúdez de Castro, JM and Martínez de Pinillos, M and Martín-Francés, L and Modesto-Mata, M and García-Campos, C and Arsuaga, JL and Martinón-Torres, M}, title = {Dental remains of the Middle Pleistocene hominins from the Sima de los Huesos site (Sierra de Atapuerca, Spain): Mandibular dentition.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.24840}, pmid = {34851548}, issn = {1932-8494}, abstract = {The Middle Pleistocene site of the Sima de los Huesos (Sierra de Atapuerca, northern Spain) has yielded a considerable number of human fossils during the period 1984-2020. Among them, up to 314 mandibular teeth have been identified. In this second paper dedicated to the dentition we present the description of the eight dental classes of the mandible following the Arizona State University Dental Anthropology System (ASUDAS) classification. In addition, we show the mean mesiodistal and buccolingual diameters obtained in these teeth compared to those of Neanderthals and a modern human sample. The morphology of both the anterior and posterior teeth suggests a close relationship of the Sima de los Huesos hominins with the populations of the second half of the Middle Pleistocene of Europe and the Near East, as well as with the so-called classic Neanderthals of Europe. The combination of dental traits in these populations is characteristic and diagnostic and suggests grouping the Sima de los Huesos hominins with the other paleodemes in a Neanderthal clade. The dental evidence of the Sima de los Huesos hominins is key to propose a complex model for the settlement of Europe during the Middle Pleistocene. In this period, different migrations of human groups probably coming from Southwest Asia, replacements, prolonged isolations, as well as hybridization and introgression processes would have contributed to the diversity of hominins in Europe.}, }
@article {pmid34839228, year = {2022}, author = {Bahain, JJ and Mercier, N and Valladas, H and Falguères, C and Masaoudi, H and Joron, JL and Froget, L and Moigne, AM and Combier, J and Moncel, MH}, title = {Reappraisal of the chronology of Orgnac 3 Lower-to-Middle Paleolithic site (Ardèche, France), a regional key sequence for the Middle Pleistocene of southern France.}, journal = {Journal of human evolution}, volume = {162}, number = {}, pages = {103092}, doi = {10.1016/j.jhevol.2021.103092}, pmid = {34839228}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Fossils ; France ; Humans ; *Neanderthals ; Technology ; *Tooth ; }, abstract = {Previous studies have suggested that the Lower-to-Middle Paleolithic transition was associated with the earliest Neanderthals, but recent research has established that the oldest Neanderthal fossils and the first signs of their technologies and behavior appear from MIS 11 or possibly earlier. To understand these changes, re-evaluation of the evidence is necessary to determine if this transition corresponds to a progressive evolution rather than abrupt change. Orgnac 3 is a key and appropriate site to study this research context. Located in southern France, it yields a long stratigraphic sequence testifying the evolution of technical and subsistence behaviors of pre-Neanderthal human groups during a Middle Pleistocene interglacial-glacial cycle. In this article, a new chronological framework is provided for the sequence based on results of dating methods applied to various types of geological materials. Speleothems and volcanic minerals, dated in previous studies by U-series and [40]Ar/[39]Ar, respectively, show periods of calcitic crystallization and regional volcanic activity. Other materials, such as heated flints and herbivore teeth, are directly related to evidence of anthropogenic activities and are analyzed in the present work by trapped-charge dating methods such as thermoluminescence and electron spin resonance combined with uranium series (ESR/U-series). The new thermoluminescence and ESR/U-series dates confirm the attribution of the Orgnac 3 stratigraphic sequence to the MIS 10-MIS 8 period and are discussed in relation to paleoenvironmental data derived from bioarchaeological studies. The paleoanthropological levels, including the emergence of Levallois technology, are dated to ca. 275 ka (early MIS 8) and appear coeval to a wet and temperate period recorded locally, the Amargiers interstadial, defined in the regional palynological records. The implications of this reassessed chronology for the archaeological assemblages are discussed in the wider context of behavioral innovations from MIS 11 onward and their establishment in subsequent periods.}, }
@article {pmid34824388, year = {2022}, author = {Brown, S and Massilani, D and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Stoessel, A and Jope-Street, B and Meyer, M and Kelso, J and Pääbo, S and Higham, T and Douka, K}, title = {The earliest Denisovans and their cultural adaptation.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {1}, pages = {28-35}, pmid = {34824388}, issn = {2397-334X}, support = {694707/ERC_/European Research Council/International ; 715069/ERC_/European Research Council/International ; 324139/ERC_/European Research Council/International ; }, mesh = {Animals ; Archaeology ; Caves ; DNA, Mitochondrial/genetics ; *Hominidae/genetics ; *Neanderthals/genetics ; }, abstract = {Since the initial identification of the Denisovans a decade ago, only a handful of their physical remains have been discovered. Here we analysed ~3,800 non-diagnostic bone fragments using collagen peptide mass fingerprinting to locate new hominin remains from Denisova Cave (Siberia, Russia). We identified five new hominin bones, four of which contained sufficient DNA for mitochondrial analysis. Three carry mitochondrial DNA of the Denisovan type and one was found to carry mtDNA of the Neanderthal type. The former come from the same archaeological layer near the base of the cave's sequence and are the oldest securely dated evidence of Denisovans at 200 ka (thousand years ago) (205-192 ka at 68.2% or 217-187 ka at 95% probability). The stratigraphic context in which they were located contains a wealth of archaeological material in the form of lithics and faunal remains, allowing us to determine the material culture associated with these early hominins and explore their behavioural and environmental adaptations. The combination of bone collagen fingerprinting and genetic analyses has so far more-than-doubled the number of hominin bones at Denisova Cave and has expanded our understanding of Denisovan and Neanderthal interactions, as well as their archaeological signatures.}, }
@article {pmid34819448, year = {2021}, author = {Dhakal, B and Makaju, R and Dhakal R, R}, title = {The Risk of COVID-19 in People Having a Particular Set of Gene.}, journal = {Kathmandu University medical journal (KUMJ)}, volume = {19}, number = {74}, pages = {265-267}, pmid = {34819448}, issn = {1812-2078}, mesh = {*COVID-19 ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Male ; Risk Factors ; SARS-CoV-2 ; }, abstract = {These risk factors of advancing age, male gender and co-existing health conditions like cancer, cardiovascular diseases, diabetes and obesity do not fully explain why some people have no or mild symptoms whereas others have severe symptoms. Genomewide association study (GWAS) identify a 3p21.31 gene cluster as a genetic susceptibility locus in patients with COVID-19 with respiratory failure. They also found a higher risk among persons with blood group A and protective effect for blood group O than among patients with other blood groups. The particular haplotype in a region of chromosome 3 is contributed to modern humans by neandertals. Another Neanderthal haplotype on chromosome 12 is associated with a 22% reduction in relative risk of becoming severely ill with COVID-19. The ApoE e4e4 homozygous genotype was found to increase the risk of severe COVID-19. Change in angiotensin converting enzyme (ACE) 2 gene was also found to be associated with increased risk of COVID-19, cardiovascular and pulmonary conditions.}, }
@article {pmid34814754, year = {2021}, author = {Mahoney, P and McFarlane, G and Smith, BH and Miszkiewicz, JJ and Cerrito, P and Liversidge, H and Mancini, L and Dreossi, D and Veneziano, A and Bernardini, F and Cristiani, E and Behie, A and Coppa, A and Bondioli, L and Frayer, DW and Radovčić, D and Nava, A}, title = {Growth of Neanderthal infants from Krapina (120-130 ka), Croatia.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1963}, pages = {20212079}, pmid = {34814754}, issn = {1471-2954}, mesh = {Animals ; Croatia ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; *Tooth ; }, abstract = {Modern humans have a slow and extended period of childhood growth, but to what extent this ontogenetic pathway was present in Neanderthals is debated. Dental development, linked to the duration of somatic growth across modern primates, is the main source for information about growth and development in a variety of fossil primates, including humans. Studies of Neanderthal permanent teeth report a pace of development either similar to recent humans or relatively accelerated. Neanderthal milk teeth, which form and emerge before permanent teeth, provide an opportunity to determine which pattern was present at birth. Here we present a comparative study of the prenatal and early postnatal growth of five milk teeth from three Neanderthals (120 000-130 000 years ago) using virtual histology. Results reveal regions of their milk teeth formed quickly before birth and over a relatively short period of time after birth. Tooth emergence commenced towards the earliest end of the eruption schedules displayed by extant human children. Advanced dental development is consistent with expectations for Neanderthal infant feeding.}, }
@article {pmid34812141, year = {2021}, author = {Williams, SA and Prang, TC and Meyer, MR and Nalley, TK and Van Der Merwe, R and Yelverton, C and García-Martínez, D and Russo, GA and Ostrofsky, KR and Spear, J and Eyre, J and Grabowski, M and Nalla, S and Bastir, M and Schmid, P and Churchill, SE and Berger, LR}, title = {New fossils of Australopithecus sediba reveal a nearly complete lower back.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34812141}, issn = {2050-084X}, mesh = {Animals ; Back/*anatomy &amp; histology ; Female ; Fossils/*anatomy &amp; histology ; Hominidae/*anatomy &amp; histology/physiology ; Locomotion ; Posture ; }, abstract = {Adaptations of the lower back to bipedalism are frequently discussed but infrequently demonstrated in early fossil hominins. Newly discovered lumbar vertebrae contribute to a near-complete lower back of Malapa Hominin 2 (MH2), offering additional insights into posture and locomotion in Australopithecus sediba. We show that MH2 possessed a lower back consistent with lumbar lordosis and other adaptations to bipedalism, including an increase in the width of intervertebral articular facets from the upper to lower lumbar column ('pyramidal configuration'). These results contrast with some recent work on lordosis in fossil hominins, where MH2 was argued to demonstrate no appreciable lordosis ('hypolordosis') similar to Neandertals. Our three-dimensional geometric morphometric (3D GM) analyses show that MH2's nearly complete middle lumbar vertebra is human-like in overall shape but its vertebral body is somewhat intermediate in shape between modern humans and great apes. Additionally, it bears long, cranially and ventrally oriented costal (transverse) processes, implying powerful trunk musculature. We interpret this combination of features to indicate that A. sediba used its lower back in both bipedal and arboreal positional behaviors, as previously suggested based on multiple lines of evidence from other parts of the skeleton and reconstructed paleobiology of A. sediba.}, }
@article {pmid34795445, year = {2021}, author = {Liston, A and Humblet-Baron, S and Duffy, D and Goris, A}, title = {Human immune diversity: from evolution to modernity.}, journal = {Nature immunology}, volume = {22}, number = {12}, pages = {1479-1489}, pmid = {34795445}, issn = {1529-2916}, support = {BBS/E/B/000C0427/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/B/000C0428/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Age Factors ; Diet ; *Evolution, Molecular ; Female ; Gene-Environment Interaction ; *Genetic Variation ; Host-Pathogen Interactions ; Humans ; Immune System/immunology/metabolism/*physiology ; Male ; Microbiota/immunology ; Sex Factors ; Species Specificity ; }, abstract = {The extreme diversity of the human immune system, forged and maintained throughout evolutionary history, provides a potent defense against opportunistic pathogens. At the same time, this immune variation is the substrate upon which a plethora of immune-associated diseases develop. Genetic analysis suggests that thousands of individually weak loci together drive up to half of the observed immune variation. Intense selection maintains this genetic diversity, even selecting for the introgressed Neanderthal or Denisovan alleles that have reintroduced variation lost during the out-of-Africa migration. Variations in age, sex, diet, environmental exposure, and microbiome each potentially explain the residual variation, with proof-of-concept studies demonstrating both plausible mechanisms and correlative associations. The confounding interaction of many of these variables currently makes it difficult to assign definitive contributions. Here, we review the current state of play in the field, identify the key unknowns in the causality of immune variation, and identify the multidisciplinary pathways toward an improved understanding.}, }
@article {pmid34779882, year = {2022}, author = {Heinzelbecker, J and Schmidt, S and Lackner, J and Busch, J and Bokemeyer, C and Classen, J and Dieing, A and Hakenberg, O and Krege, S and Papachristofilou, A and Pfister, D and Ruf, C and Schmelz, H and Schmidberger, H and Souchon, R and Winter, C and Zengerling, F and Kliesch, S and Albers, P and Oing, C}, title = {Therapy of clinical stage IIA and IIB seminoma: a systematic review.}, journal = {World journal of urology}, volume = {40}, number = {12}, pages = {2829-2841}, pmid = {34779882}, issn = {1433-8726}, mesh = {Male ; Humans ; *Seminoma/radiotherapy/drug therapy ; Retrospective Studies ; Prospective Studies ; Neoplasm Staging ; Neoplasm Recurrence, Local/pathology ; *Testicular Neoplasms/radiotherapy/drug therapy ; *Neoplasms, Second Primary/pathology ; }, abstract = {PURPOSE: The optimal treatment for clinical stage (CS) IIA/IIB seminomas is still controversial. We evaluated current treatment options.<br><br>METHODS: A systematic review was performed. Only randomized clinical trials and comparative studies published from January 2010 until February 2021 were included. Search items included: seminoma, CS IIA, CS IIB and therapy. Outcome parameters were relapse rate (RR), relapse-free (RFS), overall and cancer-specific survival (OS, CSS). Additionally, acute and long-term side effects including secondary malignancies (SMs) were analyzed.<br><br>RESULTS: Seven comparative studies (one prospective and six retrospective) were identified with a total of 5049 patients (CS IIA: 2840, CS IIB: 2209). The applied treatment modalities were radiotherapy (RT) (n&#x2009;=&#x2009;3049; CS IIA: 1888, CSIIB: 1006, unknown: 155) and chemotherapy (CT) or no RT (n&#x2009;=&#x2009;2000; CS IIA: 797, CS IIB: 1074, unknown: 129). In CS IIA, RRs ranged from 0% to 4.8% for RT and 0% for CT. Concerning CS IIB RRs of 9.5%-21.1% for RT and of 0%-14.2% for CT have been reported. 5-year OS ranged from 90 to 100%. Only two studies reported on treatment-related toxicities.<br><br>CONCLUSIONS: RT and CT are the most commonly applied treatments in CS IIA/B seminoma. In CS IIA seminomas, RRs after RT and CT are similar. However, in CS IIB, CT seems to be more effective. Survival rates of CS IIA/B seminomas are excellent. Consequently, long-term toxicities and SMs are important survivorship issues. Alternative treatment approaches, e.g., retroperitoneal lymph node dissection (RPLND) or dose-reduced sequential CT/RT are currently under prospective investigation.}, }
@article {pmid34749003, year = {2021}, author = {Sorrentino, R and Stephens, NB and Marchi, D and DeMars, LJD and Figus, C and Bortolini, E and Badino, F and Saers, JPP and Bettuzzi, M and Boschin, F and Capecchi, G and Feletti, F and Guarnieri, T and May, H and Morigi, MP and Parr, W and Ricci, S and Ronchitelli, A and Stock, JT and Carlson, KJ and Ryan, TM and Belcastro, MG and Benazzi, S}, title = {Unique foot posture in Neanderthals reflects their body mass and high mechanical stress.}, journal = {Journal of human evolution}, volume = {161}, number = {}, pages = {103093}, doi = {10.1016/j.jhevol.2021.103093}, pmid = {34749003}, issn = {1095-8606}, mesh = {Animals ; Fossils ; Humans ; *Neanderthals ; Phylogeny ; Posture ; Stress, Mechanical ; *Talus/anatomy &amp; histology ; }, abstract = {Neanderthal foot bone proportions and morphology are mostly indistinguishable from those of Homo sapiens, with the exception of several distinct Neanderthal features in the talus. The biomechanical implications of these distinct talar features remain contentious, fueling debate around the adaptive meaning of this distinctiveness. With the aim of clarifying this controversy, we test phylogenetic and behavioral factors as possible contributors, comparing tali of 10 Neanderthals and 81 H. sapiens (Upper Paleolithic and Holocene hunter-gatherers, agriculturalists, and postindustrial group) along with the Clark Howell talus (Omo, Ethiopia). Variation in external talar structures was assessed through geometric morphometric methods, while bone volume fraction and degree of anisotropy were quantified in a subsample (n = 45). Finally, covariation between point clouds of site-specific trabecular variables and surface landmark coordinates was assessed. Our results show that although Neanderthal talar external and internal morphologies were distinct from those of H. sapiens groups, shape did not significantly covary with either bone volume fraction or degree of anisotropy, suggesting limited covariation between external and internal talar structures. Neanderthal external talar morphology reflects ancestral retentions, along with various adaptations to high levels of mobility correlated to their presumably unshod hunter-gatherer lifestyle. This pairs with their high site-specific trabecular bone volume fraction and anisotropy, suggesting intense and consistently oriented locomotor loading, respectively. Relative to H.sapiens, Neanderthals exhibit differences in the talocrural joint that are potentially attributable to cultural and locomotor behavior dissimilarity, a talonavicular joint that mixes ancestral and functional traits, and a derived subtalar joint that suggests a predisposition for a pronated foot during stance phase. Overall, Neanderthal talar variation is attributable to mobility strategy and phylogenesis, while H. sapiens talar variation results from the same factors plus footwear. Our results suggest that greater Neanderthal body mass and/or higher mechanical stress uniquely led to their habitually pronated foot posture.}, }
@article {pmid34716352, year = {2021}, author = {Di Pietro, L and Barba, M and Palacios, D and Tiberio, F and Prampolini, C and Baranzini, M and Parolini, O and Arcovito, A and Lattanzi, W}, title = {Shaping modern human skull through epigenetic, transcriptional and post-transcriptional regulation of the RUNX2 master bone gene.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21316}, pmid = {34716352}, issn = {2045-2322}, mesh = {Animals ; *Biological Evolution ; Core Binding Factor Alpha 1 Subunit/*genetics/metabolism ; Cranial Sutures/growth &amp; development ; Craniosynostoses/genetics ; Epigenesis, Genetic ; Genome, Human ; Hominidae/anatomy &amp; histology/genetics ; Humans ; Mesenchymal Stem Cells ; MicroRNAs/genetics ; Neanderthals/anatomy &amp; histology/genetics ; Osteogenesis/genetics ; RNA, Long Noncoding/genetics ; Skull/*anatomy &amp; histology ; }, abstract = {RUNX2 encodes the master bone transcription factor driving skeletal development in vertebrates, and playing a specific role in craniofacial and skull morphogenesis. The anatomically modern human (AMH) features sequence changes in the RUNX2 locus compared with archaic hominins' species. We aimed to understand how these changes may have contributed to human skull globularization occurred in recent evolution. We compared in silico AMH and archaic hominins' genomes, and used mesenchymal stromal cells isolated from skull sutures of craniosynostosis patients for in vitro functional assays. We detected 459 and 470 nucleotide changes in noncoding regions of the AMH RUNX2 locus, compared with the Neandertal and Denisovan genomes, respectively. Three nucleotide changes in the proximal promoter were predicted to alter the binding of the zinc finger protein Znf263 and long-distance interactions with other cis-regulatory regions. By surface plasmon resonance, we selected nucleotide substitutions in the 3'UTRs able to affect miRNA binding affinity. Specifically, miR-3150a-3p and miR-6785-5p expression inversely correlated with RUNX2 expression during in vitro osteogenic differentiation. The expression of two long non-coding RNAs, AL096865.1 and RUNX2-AS1, within the same locus, was modulated during in vitro osteogenic differentiation and correlated with the expression of specific RUNX2 isoforms. Our data suggest that RUNX2 may have undergone adaptive phenotypic evolution caused by epigenetic and post-transcriptional regulatory mechanisms, which may explain the delayed suture fusion leading to the present-day globular skull shape.}, }
@article {pmid34716342, year = {2021}, author = {Yuan, K and Ni, X and Liu, C and Pan, Y and Deng, L and Zhang, R and Gao, Y and Ge, X and Liu, J and Ma, X and Lou, H and Wu, T and Xu, S}, title = {Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6232}, pmid = {34716342}, issn = {2041-1723}, mesh = {Algorithms ; Animals ; Asia ; DNA-Binding Proteins/genetics ; Europe ; *Genetic Introgression ; Genome, Human ; Hominidae/*genetics ; Humans ; Metagenomics/*methods ; *Models, Genetic ; Neanderthals/genetics ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Siberia ; }, abstract = {We developed a method, ArchaicSeeker 2.0, to identify introgressed hominin sequences and model multiple-wave admixture. The new method enabled us to discern two waves of introgression from both Denisovan-like and Neanderthal-like hominins in present-day Eurasian populations and an ancient Siberian individual. We estimated that an early Denisovan-like introgression occurred in Eurasia around 118.8-94.0 thousand years ago (kya). In contrast, we detected only one single episode of Denisovan-like admixture in indigenous peoples eastern to the Wallace-Line. Modeling ancient admixtures suggested an early dispersal of modern humans throughout Asia before the Toba volcanic super-eruption 74 kya, predating the initial peopling of Asia as proposed by the traditional Out-of-Africa model. Survived archaic sequences are involved in various phenotypes including immune and body mass (e.g., ZNF169), cardiovascular and lung function (e.g., HHAT), UV response and carbohydrate metabolism (e.g., HYAL1/HYAL2/HYAL3), while "archaic deserts" are enriched with genes associated with skin development and keratinization.}, }
@article {pmid34710249, year = {2022}, author = {Roksandic, M and Radović, P and Wu, XJ and Bae, CJ}, title = {Resolving the "muddle in the middle": The case for Homo bodoensis sp. nov.}, journal = {Evolutionary anthropology}, volume = {31}, number = {1}, pages = {20-29}, pmid = {34710249}, issn = {1520-6505}, mesh = {Animals ; Biological Evolution ; China ; Europe ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; }, abstract = {Recent developments in the field of palaeoanthropology necessitate the suppression of two hominin taxa and the introduction of a new species of hominins to help resolve the current nebulous state of Middle Pleistocene (Chibanian) hominin taxonomy. In particular, the poorly defined and variably understood hominin taxa Homo heidelbergensis (both sensu stricto and sensu lato) and Homo rhodesiensis need to be abandoned as they fail to reflect the full range of hominin variability in the Middle Pleistocene. Instead, we propose: (1) introduction of a new taxon, Homo bodoensis sp. nov., as an early Middle Pleistocene ancestor of the Homo sapiens lineage, with a pan-African distribution that extends into the eastern Mediterranean (Southeast Europe and the Levant); (2) that many of the fossils from Western Europe (e.g. Sima de los Huesos) currently assigned to H. heidelbergensis s.s. be reassigned to Homo neanderthalensis to reflect the early appearance of Neanderthal derived traits in the Middle Pleistocene in the region; and (3) that the Middle Pleistocene Asian fossils, particularly from China, likely represent a different lineage altogether.}, }
@article {pmid34705887, year = {2021}, author = {Zilhão, J and Angelucci, DE and Arnold, LJ and d'Errico, F and Dayet, L and Demuro, M and Deschamps, M and Fewlass, H and Gomes, L and Linscott, B and Matias, H and Pike, AWG and Steier, P and Talamo, S and Wild, EM}, title = {Revisiting the Middle and Upper Palaeolithic archaeology of Gruta do Caldeirão (Tomar, Portugal).}, journal = {PloS one}, volume = {16}, number = {10}, pages = {e0259089}, pmid = {34705887}, issn = {1932-6203}, mesh = {Animals ; Archaeology/*methods ; Fossils ; Geologic Sediments/*analysis ; Humans ; Portugal ; Radiometric Dating/*methods ; Spain ; }, abstract = {Gruta do Caldeirão features a c. 6 m-thick archaeological stratification capped by Holocene layers ABC-D and Ea, which overlie layer Eb, a deposit of Magdalenian age that underwent significant disturbance, intrusion, and component mixing caused by funerary use of the cave during the Early Neolithic. Here, we provide an updated overview of the stratigraphy and archaeological content of the underlying Pleistocene succession, whose chronology we refine using radiocarbon and single-grain optically stimulated luminescence dating. We find a high degree of stratigraphic integrity. Dating anomalies exist in association with the succession's two major discontinuities: between layer Eb and Upper Solutrean layer Fa, and between Early Upper Palaeolithic layer K and Middle Palaeolithic layer L. Mostly, the anomalies consist of older-than-expected radiocarbon ages and can be explained by bioturbation and palimpsest-forming sedimentation hiatuses. Combined with palaeoenvironmental inferences derived from magnetic susceptibility analyses, the dating shows that sedimentation rates varied in tandem with the oscillations in global climate revealed by the Greenland oxygen isotope record. A steep increase in sedimentation rate is observed through the Last Glacial Maximum, resulting in a c. 1.5 m-thick accumulation containing conspicuous remains of occupation by people of the Solutrean technocomplex, whose traditional subdivision is corroborated: the index fossils appear in the expected stratigraphic order; the diagnostics of the Protosolutrean and the Lower Solutrean predate 24,000 years ago; and the constraints on the Upper Solutrean place it after Greenland Interstadial 2.2. (23,220-23,340 years ago). Human usage of the site during the Early Upper and the Middle Palaeolithic is episodic and low-intensity: stone tools are few, and the faunal remains relate to carnivore activity. The Middle Palaeolithic is found to persist beyond 39,000 years ago, at least three millennia longer than in the Franco-Cantabrian region. This conclusion is upheld by Bayesian modelling and stands even if the radiocarbon ages for the Middle Palaeolithic levels are removed from consideration (on account of observed inversions and the method's potential for underestimation when used close to its limit of applicability). A number of localities in Spain and Portugal reveal a similar persistence pattern. The key evidence comes from high-resolution fluviatile contexts spared by the site formation issues that our study of Caldeirão brings to light-palimpsest formation, post-depositional disturbance, and erosion. These processes. are ubiquitous in the cave and rock-shelter sites of Iberia, reflecting the impact on karst archives of the variation in climate and environments that occurred through the Upper Pleistocene, and especially at two key points in time: between 37,000 and 42,000 years ago, and after the Last Glacial Maximum. Such empirical difficulties go a long way towards explaining the controversies surrounding the associated cultural transitions: from the Middle to the Upper Palaeolithic, and from the Solutrean to the Magdalenian. Alongside potential dating error caused by incomplete decontamination, proper consideration of sample association issues is required if we are ever to fully understand what happened with the human settlement of Iberia during these critical intervals, and especially so with regards to the fate of Iberia's last Neandertal populations.}, }
@article {pmid34702870, year = {2021}, author = {Mahadevan, J and Pathak, AK and Vemula, A and Nadella, RK and Viswanath, B and Jain, S and ,  and Purushottam, M and Mondal, M}, title = {Analysis of whole exome sequencing in severe mental illness hints at selection of brain development and immune related genes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21088}, pmid = {34702870}, issn = {2045-2322}, mesh = {Animals ; *Brain/growth &amp; development/immunology ; Female ; Humans ; Immunity, Innate/*genetics ; Male ; *Mental Disorders/genetics/immunology ; Neanderthals/genetics/immunology ; *Whole Exome Sequencing ; }, abstract = {Evolutionary trends may underlie some aspects of the risk for common, non-communicable disorders, including psychiatric disease. We analyzed whole exome sequencing data from 80 unique individuals from India coming from families with two or more individuals with severe mental illness. We used Population Branch Statistics (PBS) to identify variants and genes under positive selection and identified 74 genes as candidates for positive selection. Of these, 20 were previously associated with Schizophrenia, Alzheimer's disease and cognitive abilities in genome wide association studies. We then checked whether any of these 74 genes were involved in common biological pathways or related to specific cellular or molecular functions. We found that immune related pathways and functions related to innate immunity such as antigen binding were over-represented. We also evaluated for the presence of Neanderthal introgressed segments in these genes and found Neanderthal introgression in a single gene out of the 74 candidate genes. However, the introgression pattern indicates the region is unlikely to be the source for selection. Our findings hint at how selection pressures in individuals from families with a history of severe mental illness may diverge from the general population. Further, it also provides insights into the genetic architecture of severe mental illness, such as schizophrenia and its link to immune factors.}, }
@article {pmid34662402, year = {2022}, author = {Jagoda, E and Xue, JR and Reilly, SK and Dannemann, M and Racimo, F and Huerta-Sanchez, E and Sankararaman, S and Kelso, J and Pagani, L and Sabeti, PC and Capellini, TD}, title = {Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells.}, journal = {Molecular biology and evolution}, volume = {39}, number = {1}, pages = {}, pmid = {34662402}, issn = {1537-1719}, support = {R35 GM125055/GM/NIGMS NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Gene Expression ; *Genetic Variation ; *Genome, Human ; Humans ; Immunity, Innate/*genetics ; Inflammation ; *Neanderthals/genetics ; }, abstract = {Although some variation introgressed from Neanderthals has undergone selective sweeps, little is known about its functional significance. We used a Massively Parallel Reporter Assay (MPRA) to assay 5,353 high-frequency introgressed variants for their ability to modulate the gene expression within 170 bp of endogenous sequence. We identified 2,548 variants in active putative cis-regulatory elements (CREs) and 292 expression-modulating variants (emVars). These emVars are predicted to alter the binding motifs of important immune transcription factors, are enriched for associations with neutrophil and white blood cell count, and are associated with the expression of genes that function in innate immune pathways including inflammatory response and antiviral defense. We combined the MPRA data with other data sets to identify strong candidates to be driver variants of positive selection including an emVar that may contribute to protection against severe COVID-19 response. We endogenously deleted two CREs containing expression-modulation variants linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2, respectively, three genes differentially expressed during influenza infection. Overall, we present the first database of experimentally identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans.}, }
@article {pmid34634929, year = {2021}, author = {Chen, T and Lin, YX and Zha, Y and Sun, Y and Tian, J and Yang, Z and Lin, SW and Yu, F and Chen, ZS and Kuang, BH and Lei, JJ and Nie, YJ and Xu, Y and Tian, DB and Li, YZ and Yang, B and Xu, Q and Yang, L and Zhong, N and Zheng, M and Li, Y and Zhao, J and Zhang, XY and Feng, L}, title = {A Low-Producing Haplotype of Interleukin-6 Disrupting CTCF Binding Is Protective against Severe COVID-19.}, journal = {mBio}, volume = {12}, number = {5}, pages = {e0137221}, pmid = {34634929}, issn = {2150-7511}, mesh = {A549 Cells ; COVID-19/*metabolism/*prevention &amp; control ; Genotype ; Haplotypes/genetics ; HeLa Cells ; Humans ; Interleukin-6/genetics/*metabolism ; Polymorphism, Single Nucleotide/genetics ; Real-Time Polymerase Chain Reaction ; Software ; }, abstract = {Interleukin6 (IL-6) is a key driver of hyperinflammation in COVID-19, and its level strongly correlates with disease progression. To investigate whether variability in COVID-19 severity partially results from differential IL-6 expression, functional single-nucleotide polymorphisms (SNPs) of IL-6 were determined in Chinese COVID-19 patients with mild or severe illness. An Asian-common IL-6 haplotype defined by promoter SNP rs1800796 and intronic SNPs rs1524107 and rs2066992 correlated with COVID-19 severity. Homozygote carriers of C-T-T variant haplotype were at lower risk of developing severe symptoms (odds ratio, 0.256; 95% confidence interval, 0.088 to 0.739; P = 0.007). This protective haplotype was associated with lower levels of IL-6 and its antisense long noncoding RNA IL-6-AS1 by cis-expression quantitative trait loci analysis. The differences in expression resulted from the disturbance of stimulus-dependent bidirectional transcription of the IL-6/IL-6-AS1 locus by the polymorphisms. The protective rs2066992-T allele disrupted a conserved CTCF-binding locus at the enhancer elements of IL-6-AS1, which transcribed antisense to IL-6 and induces IL-6 expression in inflammatory responses. As a result, carriers of the protective allele had significantly reduced IL-6-AS1 expression and attenuated IL-6 induction in response to acute inflammatory stimuli and viral infection. Intriguingly, this low-producing variant that is endemic to present-day Asia was found in early humans who had inhabited mainland Asia since ∼40,000 years ago but not in other ancient humans, such as Neanderthals and Denisovans. The present study suggests that an individual's IL-6 genotype underlies COVID-19 outcome and may be used to guide IL-6 blockade therapy in Asian patients. IMPORTANCE Overproduction of cytokine interleukin-6 (IL-6) is a hallmark of severe COVID-19 and is believed to play a critical role in exacerbating the excessive inflammatory response. Polymorphisms in IL-6 account for the variability of IL-6 expression and disparities in infectious diseases, but its contribution to the clinical presentation of COVID-19 has not been reported. Here, we investigated IL-6 polymorphisms in severe and mild cases of COVID-19 in a Chinese population. The variant haplotype C-T-T, represented by rs1800796, rs1524107, and rs2066992 at the IL-6 locus, was reduced in patients with severe illness; in contrast, carriers of the wild-type haplotype G-C-G had higher risk of severe illness. Mechanistically, the protective variant haplotype lost CTCF binding at the IL-6 intron and responded poorly to inflammatory stimuli, which may protect the carriers from hyperinflammation in response to acute SARS-CoV-2 infection. These results point out the possibility that IL-6 genotypes underlie the differential viral virulence during the outbreak of COVID-19. The risk loci we identified may serve as a genetic marker to screen high-risk COVID-19 patients.}, }
@article {pmid34622284, year = {2021}, author = {Villanea, FA and Huerta-Sanchez, E and Fox, K}, title = {Corrigendum to: ABO Genetic Variation in Neanderthals and Denisovans.}, journal = {Molecular biology and evolution}, volume = {38}, number = {12}, pages = {5835}, doi = {10.1093/molbev/msab261}, pmid = {34622284}, issn = {1537-1719}, }
@article {pmid34616690, year = {2021}, author = {Shiba, T and Komatsu, K and Sudo, T and Sawafuji, R and Saso, A and Ueda, S and Watanabe, T and Nemoto, T and Kano, C and Nagai, T and Ohsugi, Y and Katagiri, S and Takeuchi, Y and Kobayashi, H and Iwata, T}, title = {Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {723821}, pmid = {34616690}, issn = {2235-2988}, mesh = {Actinobacteria ; Actinomyces ; Bacteria/*classification ; Fusobacterium ; History, 17th Century ; History, 18th Century ; History, 19th Century ; Humans ; Japan ; *Periodontitis/diagnosis/history/microbiology ; Porphyromonas gingivalis ; Prevotella ; Treponema ; X-Ray Microtomography ; }, abstract = {Ancient dental calculus, formed from dental plaque, is a rich source of ancient DNA and can provide information regarding the food and oral microbiology at that time. Genomic analysis of dental calculus from Neanderthals has revealed the difference in bacterial composition of oral microbiome between Neanderthals and modern humans. There are few reports investigating whether the pathogenic bacteria of periodontitis, a polymicrobial disease induced in response to the accumulation of dental plaque, were different between ancient and modern humans. This study aimed to compare the bacterial composition of the oral microbiome in ancient and modern human samples and to investigate whether lifestyle differences depending on the era have altered the bacterial composition of the oral microbiome and the causative bacteria of periodontitis. Additionally, we introduce a novel diagnostic approach for periodontitis in ancient skeletons using micro-computed tomography. Ancient 16S rDNA sequences were obtained from 12 samples at the Unko-in site (18th-19th century) of the Edo era (1603-1867), a characteristic period in Japan when immigrants were not accepted. Furthermore, modern 16S rDNA data from 53 samples were obtained from a database to compare the modern and ancient microbiome. The microbial co-occurrence network was analyzed based on 16S rDNA read abundance. Eubacterium species, Mollicutes species, and Treponema socranskii were the core species in the Edo co-occurrence network. The co-occurrence relationship between Actinomyces oricola and Eggerthella lenta appeared to have played a key role in causing periodontitis in the Edo era. However, Porphyromonas gingivalis, Fusobacterium nucleatum subsp. vincentii, and Prevotella pleuritidis were the core and highly abundant species in the co-occurrence network of modern samples. These results suggest the possibility of differences in the pathogens causing periodontitis during different eras in history.}, }
@article {pmid34615929, year = {2021}, author = {Rothschild, B and Haeusler, M}, title = {Possible vertebral brucellosis infection in a Neanderthal.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19846}, pmid = {34615929}, issn = {2045-2322}, mesh = {Animals ; Brucellosis/*diagnosis/*microbiology ; Imaging, Three-Dimensional ; Male ; *Neanderthals ; Osteoarthritis/*diagnosis/*microbiology ; Skeleton ; Spine/diagnostic imaging/*microbiology/*pathology ; Tomography, X-Ray Computed ; }, abstract = {The La Chapelle-aux-Saints 1 skeleton of an old (>60-year-old) male Neanderthal is renowned for the advanced osteoarthritis of its spinal column and hip joint, and their implications for posture and lifestyle in these Mid- to Late Pleistocene humans. Reassessment of the pathologic lesions reveals erosions at multiple non-contiguous vertebrae and reactive bone formation extending far beyond the left hip joint, which suggests the additional diagnosis of brucellosis. This implies the earliest secure evidence of this zoonotic disease in hominin evolution. Brucellosis might have been transmitted via butchering or eating raw meat and is well compatible with the range of prey animals documented for Neanderthals. The associated infertility could have represented an important aspect of health in these late archaic humans.}, }
@article {pmid36465976, year = {2021}, author = {Smith, R and Moots, RJ and Murad, M and Wallace, GR}, title = {A Darwinian View of Behçet's Disease.}, journal = {Rheumatology and immunology research}, volume = {2}, number = {2}, pages = {91-99}, pmid = {36465976}, issn = {2719-4523}, abstract = {Behçet's disease (BD) is a multisystem inflammatory disorder of unknown etiology, characterized by oral and genital ulceration, with other complications including eye, skin, joint, and central nervous system (CNS) lesions. Diagnosis is based on clinical findings, which may differ between patients. There is a strong genetic basis for BD; however, only a few genes have been associated with the disease across the geographical spread of BD. In this article, we discuss the history and combination of genes involved in this complex disease in relation to the geographical range and present our view that the disease has developed from a Darwinian perspective, with different gene polymorphisms that affect the same biological pathway. Moreover, these mutations individually are protective mechanisms against the disease relevant to each region, which affected both archaic and modern humans.}, }
@article {pmid34570765, year = {2021}, author = {Findley, AS and Zhang, X and Boye, C and Lin, YL and Kalita, CA and Barreiro, L and Lohmueller, KE and Pique-Regi, R and Luca, F}, title = {A signature of Neanderthal introgression on molecular mechanisms of environmental responses.}, journal = {PLoS genetics}, volume = {17}, number = {9}, pages = {e1009493}, pmid = {34570765}, issn = {1553-7404}, support = {F30 GM131580/GM/NIGMS NIH HHS/United States ; R01 GM109215/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Alleles ; Animals ; *Environmental Exposure ; Gene Expression Regulation ; *Genome, Human ; Human Migration ; Humans ; Neanderthals/*genetics ; Polymorphism, Single Nucleotide ; Protein Binding ; Quantitative Trait Loci ; Transcription Factors/metabolism ; }, abstract = {Ancient human migrations led to the settlement of population groups in varied environmental contexts worldwide. The extent to which adaptation to local environments has shaped human genetic diversity is a longstanding question in human evolution. Recent studies have suggested that introgression of archaic alleles in the genome of modern humans may have contributed to adaptation to environmental pressures such as pathogen exposure. Functional genomic studies have demonstrated that variation in gene expression across individuals and in response to environmental perturbations is a main mechanism underlying complex trait variation. We considered gene expression response to in vitro treatments as a molecular phenotype to identify genes and regulatory variants that may have played an important role in adaptations to local environments. We investigated if Neanderthal introgression in the human genome may contribute to the transcriptional response to environmental perturbations. To this end we used eQTLs for genes differentially expressed in a panel of 52 cellular environments, resulting from 5 cell types and 26 treatments, including hormones, vitamins, drugs, and environmental contaminants. We found that SNPs with introgressed Neanderthal alleles (N-SNPs) disrupt binding of transcription factors important for environmental responses, including ionizing radiation and hypoxia, and for glucose metabolism. We identified an enrichment for N-SNPs among eQTLs for genes differentially expressed in response to 8 treatments, including glucocorticoids, caffeine, and vitamin D. Using Massively Parallel Reporter Assays (MPRA) data, we validated the regulatory function of 21 introgressed Neanderthal variants in the human genome, corresponding to 8 eQTLs regulating 15 genes that respond to environmental perturbations. These findings expand the set of environments where archaic introgression may have contributed to adaptations to local environments in modern humans and provide experimental validation for the regulatory function of introgressed variants.}, }
@article {pmid34559564, year = {2021}, author = {Saitou, M and Resendez, S and Pradhan, AJ and Wu, F and Lie, NC and Hall, NJ and Zhu, Q and Reinholdt, L and Satta, Y and Speidel, L and Nakagome, S and Hanchard, NA and Churchill, G and Lee, C and Atilla-Gokcumen, GE and Mu, X and Gokcumen, O}, title = {Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor.}, journal = {Science advances}, volume = {7}, number = {39}, pages = {eabi4476}, pmid = {34559564}, issn = {2375-2548}, support = {/WT_/Wellcome Trust/United Kingdom ; P30 AG038070/AG/NIA NIH HHS/United States ; R01 EY020545/EY/NEI NIH HHS/United States ; R01 EY029705/EY/NEI NIH HHS/United States ; }, abstract = {The common deletion of the third exon of the growth hormone receptor gene (GHRd3) in humans is associated with birth weight, growth after birth, and time of puberty. However, its evolutionary history and the molecular mechanisms through which it affects phenotypes remain unresolved. We present evidence that this deletion was nearly fixed in the ancestral population of anatomically modern humans and Neanderthals but underwent a recent adaptive reduction in frequency in East Asia. We documented that GHRd3 is associated with protection from severe malnutrition. Using a novel mouse model, we found that, under calorie restriction, Ghrd3 leads to the female-like gene expression in male livers and the disappearance of sexual dimorphism in weight. The sex- and diet-dependent effects of GHRd3 in our mouse model are consistent with a model in which the allele frequency of GHRd3 varies throughout human evolution as a response to fluctuations in resource availability.}, }
@article {pmid34554811, year = {2021}, author = {Liu, Y and Mao, X and Krause, J and Fu, Q}, title = {Insights into human history from the first decade of ancient human genomics.}, journal = {Science (New York, N.Y.)}, volume = {373}, number = {6562}, pages = {1479-1484}, doi = {10.1126/science.abi8202}, pmid = {34554811}, issn = {1095-9203}, mesh = {Africa ; Americas ; Animals ; Asia ; Biological Evolution ; *DNA, Ancient ; Europe ; *Genome, Human ; *Genomics ; History, Ancient ; Human Migration ; Humans ; Neanderthals/genetics ; Oceania ; *Population Dynamics ; Siberia ; }, abstract = {Recent advancements in DNA sequencing technologies and laboratory preparation protocols have rapidly expanded the scope of ancient DNA research over the past decade, both temporally and geographically. Discoveries include interactions between archaic and modern humans as well as modern human population dynamics, including those coinciding with the Last Glacial Maximum and the settlement history of most world regions. This new type of data allows us to examine the deep past of human population dynamics and sharpen the current understanding of our present. The continued development in the ancient DNA field has transformed our understanding of human genetic history and will keep uncovering the further mysteries of our recent evolutionary past.}, }
@article {pmid34534904, year = {2021}, author = {Keller, M and Hagag, IT and Balzer, J and Beyer, K and Kersebohm, JC and Sadeghi, B and Wernike, K and Höper, D and Wylezich, C and Beer, M and Groschup, MH}, title = {Detection of SARS-CoV-2 variant B.1.1.7 in a cat in Germany.}, journal = {Research in veterinary science}, volume = {140}, number = {}, pages = {229-232}, doi = {10.1016/j.rvsc.2021.09.008}, pmid = {34534904}, issn = {1532-2661}, mesh = {Animals ; *COVID-19/veterinary ; *Cat Diseases/diagnosis ; Cats ; Germany ; Humans ; Real-Time Polymerase Chain Reaction/veterinary ; SARS-CoV-2 ; }, abstract = {Several non-variant of concern SARS-CoV-2 infections in pets have been reported as documented in the OIE and GISAID databases and there is only one fully documented case of an alpha variant of concern (VOC)(B.1.1.7) in the United States so far. Here, we describe the first case in a cat infected with the alpha SARS-CoV-2 variant in Germany. A cat suffering from pneumonia was presented to a veterinary practice. The pneumonia was treated symptomatically, but 16 days later the cat was presented again. Since the owner had been tested positive for a SARS-CoV-2 infection in the meantime, swab samples were taken from the cat and analyzed for SARS-CoV-2 specific nucleic acids. The various RT-qPCR analyses and whole-genome sequencing revealed the presence of the SARS-CoV-2 B.1.1.7 variant in this cat. This study shows that pets living in close contact with SARS-CoV-2 B.1.1.7 infected owners can contract this virus and also suffer from a respiratory disease. It is not clear yet whether onward transmissions to other cats and humans can occur. To minimize transmission risks, pet owners and veterinarians should comply to the hygienic rules published by OIE and others. It must be stated, that infections of cats with SARS-CoV-2 is still a rare event. Cats with clinical signs of a respiratory disease should be presented to a veterinarian, who will decide on further steps.}, }
@article {pmid34531420, year = {2021}, author = {Neto de Carvalho, C and Belaústegui, Z and Toscano, A and Muñiz, F and Belo, J and Galán, JM and Gómez, P and Cáceres, LM and Rodríguez-Vidal, J and Cunha, PP and Cachão, M and Ruiz, F and Ramirez-Cruzado, S and Giles-Guzmán, F and Finlayson, G and Finlayson, S and Finlayson, C}, title = {First tracks of newborn straight-tusked elephants (Palaeoloxodon antiquus).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {17311}, pmid = {34531420}, issn = {2045-2322}, mesh = {Animals ; Animals, Newborn ; Body Height ; Body Weight ; Ecosystem ; Elephants/anatomy &amp; histology/*physiology ; Female ; Geography ; Humans ; Imaging, Three-Dimensional ; Neanderthals ; Reproduction ; Spain ; }, abstract = {Tracks and trackways of newborns, calves and juveniles attributed to straight-tusked elephants were found in the MIS 5 site (Upper Pleistocene) known as the Matalascañas Trampled Surface (MTS) at Huelva, SW Spain. Evidence of a snapshot of social behaviour, especially parental care, can be determined from the concentration of elephant tracks and trackways, and especially from apparently contemporaneous converging trackways, of small juvenile and larger, presumably young adult female tracks. The size frequency of the tracks enabled us to infer body mass and age distribution of the animals that crossed the MTS. Comparisons of the MTS demographic frequency with the morphology of the fore- and hind limbs of extant and fossil proboscideans shed light into the reproductive ecology of the straight-tusked elephant, Palaeloxodon antiquus. The interdune pond habitat appeared to have been an important water and food resource for matriarchal herds of straight-tusked elephants and likely functioned as a reproductive habitat, with only the rare presence of adult and older males in the MTS. The preservation of this track record in across a paleosol surface, although heavily trampled by different animals, including Neanderthals, over a short time frame, permitted an exceptional view into short-term intraspecific trophic interactions occurring in the Last Interglacial coastal habitat. Therefore, it is hypothesized that Neanderthals visited MTS for hunting or scavenging on weakened or dead elephants, and more likely calves.}, }
@article {pmid34528508, year = {2021}, author = {Yan, SM and Sherman, RM and Taylor, DJ and Nair, DR and Bortvin, AN and Schatz, MC and McCoy, RC}, title = {Local adaptation and archaic introgression shape global diversity at human structural variant loci.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34528508}, issn = {2050-084X}, support = {R35 GM133747/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Asians ; *Evolution, Molecular ; Gene Flow ; *Genome, Human ; Genomics ; *Genotype ; Haplotypes/genetics ; Humans ; Linkage Disequilibrium ; Neanderthals/genetics ; Selection, Genetic ; }, abstract = {Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation - a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.}, }
@article {pmid34521476, year = {2021}, author = {Árnason, &#xda;}, title = {The unidirectional phylogeny of Homo sapiens anchors the origin of modern humans in Eurasia.}, journal = {Hereditas}, volume = {158}, number = {1}, pages = {36}, pmid = {34521476}, issn = {1601-5223}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetics, Population ; Haplotypes ; *Hominidae ; Humans ; *Neanderthals/genetics ; Phylogeny ; }, abstract = {BACKGROUND: The Out of Africa hypothesis, OOAH, was challenged recently in an extended mtDNA analysis, PPA (Progressive Phylogenetic Analysis), that identified the African human populations as paraphyletic, a finding that contradicted the common OOAH understanding that Hss had originated in Africa and invaded Eurasia from there. The results were consistent with the molecular Out of Eurasia hypothesis, OOEH, and Eurasian palaeontology, a subject that has been largely disregarded in the discussion of OOAH.<br><br>RESULTS: In the present study the mtDNA tree, a phylogeny based on maternal inheritance, was compared to the nuclear DNA tree of the paternally transmitted Y-chromosome haplotypes, Y-DNAs. The comparison showed full phylogenetic coherence between these two separate sets of data. The results were consistent with potentially four translocations of modern humans from Eurasia into Africa, the earliest taking place &#x2248; 250,000&#xa0;years before present, YBP. The results were in accordance with the postulates behind OOEH at the same time as they lent no support to the OOAH.<br><br>CONCLUSIONS: The conformity between the mtDNA and Y-DNA phylogenies of Hss is consistent with the understanding that Eurasia was the donor and not the receiver in human evolution. The evolutionary problems related to OOAH became similarly exposed by the mtDNA introgression that took place from Hss into Neanderthals &#x2248; 500,000 YBP, a circumstance that demonstrated the early coexistence of the two lineages in Eurasia.}, }
@article {pmid34493715, year = {2021}, author = {Coll Macià, M and Skov, L and Peter, BM and Schierup, MH}, title = {Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5317}, pmid = {34493715}, issn = {2041-1723}, mesh = {Animals ; Asia ; Crosses, Genetic ; DNA, Ancient/*analysis ; Europe ; Female ; *Gene Flow ; *Genome, Human ; History, 21st Century ; History, Ancient ; Humans ; Male ; *Mutation ; Neanderthals/*genetics ; Polymorphism, Restriction Fragment Length ; }, abstract = {After the main Out-of-Africa event, humans interbred with Neanderthals leaving 1-2% of Neanderthal DNA scattered in small fragments in all non-African genomes today. Here we investigate what can be learned about human demographic processes from the size distribution of these fragments. We observe differences in fragment length across Eurasia with 12% longer fragments in East Asians than West Eurasians. Comparisons between extant populations with ancient samples show that these differences are caused by different rates of decay in length by recombination since the Neanderthal admixture. In concordance, we observe a strong correlation between the average fragment length and the mutation accumulation, similar to what is expected by changing the ages at reproduction as estimated from trio studies. Altogether, our results suggest differences in the generation interval across Eurasia, by up 10-20%, over the past 40,000 years. We use sex-specific mutation signatures to infer whether these changes were driven by shifts in either male or female age at reproduction, or both. We also find that previously reported variation in the mutational spectrum may be largely explained by changes to the generation interval. We conclude that Neanderthal fragment lengths provide unique insight into differences among human populations over recent history.}, }
@article {pmid34492092, year = {2021}, author = {Çep, B and Schürch, B and Münzel, SC and Frick, JA}, title = {Adaptive capacity and flexibility of the Neanderthals at Heidenschmiede (Swabian Jura) with regard to core reduction strategies.}, journal = {PloS one}, volume = {16}, number = {9}, pages = {e0257041}, pmid = {34492092}, issn = {1932-6203}, mesh = {*Adaptation, Physiological ; Animals ; *Archaeology ; Fossils ; Imaging, Three-Dimensional ; Neanderthals/*physiology ; Radiometric Dating ; }, abstract = {The branched reduction system at the Heidenschmiede described here is hitherto exceptional for the Middle Paleolithic of the Swabian Jura. By means of refits and supporting objects, we are able to describe a superordinate reduction system that combines several individual reduction concepts, such as Levallois and blade production, within one volume. In the Middle Paleolithic of the Swabian Jura, blade technology has thus far played a rather minor role. On the one hand, it is possible to split a selected volume (nodule) into three parts, which are reduced separately according to individual concepts. On the other hand, it is also possible to reduce parts of a volume with one concept first and then with another. The hypothetical reduction system can be branched or linear, thus emphasizing the technological flexibility in core reduction, which requires a high degree of cognitive skills of three-dimensional imagination.}, }
@article {pmid34487600, year = {2021}, author = {Gregory, MD and Eisenberg, DP and Hamborg, M and Kippenhan, JS and Kohn, P and Kolachana, B and Dickinson, D and Berman, KF}, title = {Neanderthal-derived genetic variation in living humans relates to schizophrenia diagnosis, to psychotic symptom severity, and to dopamine synthesis.}, journal = {American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics}, volume = {186}, number = {5}, pages = {329-338}, pmid = {34487600}, issn = {1552-485X}, support = {ZIA MH002717/ImNIH/Intramural NIH HHS/United States ; U01 MH079469/MH/NIMH NIH HHS/United States ; R01 MH067257/MH/NIMH NIH HHS/United States ; R01 MH059587/MH/NIMH NIH HHS/United States ; R01 MH059586/MH/NIMH NIH HHS/United States ; R01 MH059566/MH/NIMH NIH HHS/United States ; R01 MH060879/MH/NIMH NIH HHS/United States ; R01 MH061675/MH/NIMH NIH HHS/United States ; Z99 MH999999/ImNIH/Intramural NIH HHS/United States ; R01 MH084098/MH/NIMH NIH HHS/United States ; U01 MH046276/MH/NIMH NIH HHS/United States ; R01 MH060870/MH/NIMH NIH HHS/United States ; R01 MH081800/MH/NIMH NIH HHS/United States ; ZIA MH002652/ImNIH/Intramural NIH HHS/United States ; R01 MH059571/MH/NIMH NIH HHS/United States ; R01 MH059565/MH/NIMH NIH HHS/United States ; U01 MH079470/MH/NIMH NIH HHS/United States ; ZIA MH002942/ImNIH/Intramural NIH HHS/United States ; U01 MH046289/MH/NIMH NIH HHS/United States ; RC2 MH089964/MH/NIMH NIH HHS/United States ; R01 MH059588/MH/NIMH NIH HHS/United States ; U01 MH046318/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Dopamine ; Genetic Variation ; *Hominidae ; Humans ; *Neanderthals/genetics ; *Psychotic Disorders/diagnosis/genetics ; *Schizophrenia/diagnosis/genetics ; }, abstract = {Schizophrenia has been hypothesized to be a human-specific condition, but experimental approaches to testing this idea have been limited. Because Neanderthals, our closest evolutionary relatives, interbred with modern humans prior to their disappearance from the fossil record, leaving a residual echo that survives in our DNA today, we leveraged new discoveries about ancient hominid DNA to explore this hypothesis in living people in three converging ways. First, in four independent case-control datasets totaling 9,362 individuals, individuals with schizophrenia had less Neanderthal-derived genetic variation than controls (p = .044). Second, in 49 unmedicated inpatients with schizophrenia, having more Neanderthal admixture predicted less severe positive symptoms (p = .046). Finally, using [18] F-fluorodopa PET scanning in 172 healthy individuals, having greater Neanderthal introgression was significantly associated with lower dopamine synthesis capacity in the striatum and pons (p's < 2 × 10[-5]), which is fundamentally important in the pathophysiology and treatment of psychosis. These results may help to elucidate the evolutionary history of a devastating neuropsychiatric disease by supporting the notion of schizophrenia as a human-specific condition. Additionally, the relationship between Neanderthal admixture and dopamine function suggests a potential mechanism whereby Neanderthal admixture may have affected our gene pool to alter schizophrenia risk and/or course.}, }
@article {pmid34480555, year = {2021}, author = {Ferreira, JC and Alshamali, F and Montinaro, F and Cavadas, B and Torroni, A and Pereira, L and Raveane, A and Fernandes, V}, title = {Projecting Ancient Ancestry in Modern-Day Arabians and Iranians: A Key Role of the Past Exposed Arabo-Persian Gulf on Human Migrations.}, journal = {Genome biology and evolution}, volume = {13}, number = {9}, pages = {}, pmid = {34480555}, issn = {1759-6653}, mesh = {Animals ; DNA, Ancient ; Genetics, Population ; Genome, Human ; Human Migration ; Humans ; Indian Ocean ; Iran ; *Neanderthals/genetics ; }, abstract = {The Arabian Peninsula is strategic for investigations centered on the early structuring of modern humans in the wake of the out-of-Africa migration. Despite its poor climatic conditions for the recovery of ancient human DNA evidence, the availability of both genomic data from neighboring ancient specimens and informative statistical tools allow modeling the ancestry of local modern populations. We applied this approach to a data set of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking western Arabia with the Levant, and eastern Arabia with Iran and the Caucasus. Eastern Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for a possible bias due to a recent sub-Saharan African input in their genomes. Not surprisingly, eastern Arabians were also the ones with highest similarity with Iberomaurusians, who were, so far, the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans who diverged from the common European-eastern Asian pool before 50,000 years ago, prior to the later interbred with Neanderthals. Our results appear to indicate that the exposed basin of the Arabo-Persian Gulf was the possible home of basal Eurasians, a scenario to be further investigated by searching ancient Arabian human specimens.}, }
@article {pmid34475260, year = {2021}, author = {Warinner, C and Velsko, IM and Fellows Yates, JA}, title = {Reply to Ben-Dor et al.: Oral bacteria of Neanderthals and modern humans exhibit evidence of starch adaptation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {37}, pages = {}, pmid = {34475260}, issn = {1091-6490}, mesh = {Animals ; Archaeology ; Bacteria ; *Hominidae ; Humans ; *Neanderthals ; Starch ; }, }
@article {pmid34471286, year = {2021}, author = {Groucutt, HS and White, TS and Scerri, EML and Andrieux, E and Clark-Wilson, R and Breeze, PS and Armitage, SJ and Stewart, M and Drake, N and Louys, J and Price, GJ and Duval, M and Parton, A and Candy, I and Carleton, WC and Shipton, C and Jennings, RP and Zahir, M and Blinkhorn, J and Blockley, S and Al-Omari, A and Alsharekh, AM and Petraglia, MD}, title = {Multiple hominin dispersals into Southwest Asia over the past 400,000 years.}, journal = {Nature}, volume = {597}, number = {7876}, pages = {376-380}, pmid = {34471286}, issn = {1476-4687}, support = {//European Research Council/International ; }, mesh = {Animals ; Anthropology ; Arabia ; Asia ; History, Ancient ; *Hominidae ; Human Migration/*history ; Paleontology ; Tool Use Behavior ; }, abstract = {Pleistocene hominin dispersals out of, and back into, Africa necessarily involved traversing the diverse and often challenging environments of Southwest Asia[1-4]. Archaeological and palaeontological records from the Levantine woodland zone document major biological and cultural shifts, such as alternating occupations by Homo sapiens and Neanderthals. However, Late Quaternary cultural, biological and environmental records from the vast arid zone that constitutes most of Southwest Asia remain scarce, limiting regional-scale insights into changes in hominin demography and behaviour[1,2,5]. Here we report a series of dated palaeolake sequences, associated with stone tool assemblages and vertebrate fossils, from the Khall Amayshan 4 and Jubbah basins in the Nefud Desert. These findings, including the oldest dated hominin occupations in Arabia, reveal at least five hominin expansions into the Arabian interior, coinciding with brief 'green' windows of reduced aridity approximately 400, 300, 200, 130-75 and 55 thousand years ago. Each occupation phase is characterized by a distinct form of material culture, indicating colonization by diverse hominin groups, and a lack of long-term Southwest Asian population continuity. Within a general pattern of African and Eurasian hominin groups being separated by Pleistocene Saharo-Arabian aridity, our findings reveal the tempo and character of climatically modulated windows for dispersal and admixture.}, }
@article {pmid34455262, year = {2021}, author = {Buck, LT and Katz, DC and Ackermann, RR and Hlusko, LJ and Kanthaswamy, S and Weaver, TD}, title = {Effects of hybridization on pelvic morphology: A macaque model.}, journal = {Journal of human evolution}, volume = {159}, number = {}, pages = {103049}, doi = {10.1016/j.jhevol.2021.103049}, pmid = {34455262}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Fossils ; *Hominidae ; Macaca ; *Neanderthals ; Pelvis ; }, abstract = {Ancient DNA analyses have shown that interbreeding between hominin taxa occurred multiple times. Although admixture is often reflected in skeletal phenotype, the relationship between the two remains poorly understood, hampering interpretation of the hominin fossil record. Direct study of this relationship is often impossible due to the paucity of hominin fossils and difficulties retrieving ancient genetic material. Here, we use a sample of known ancestry hybrids between two closely related nonhuman primate taxa (Indian and Chinese Macaca mulatta) to investigate the effect of admixture on skeletal morphology. We focus on pelvic shape, which has potential fitness implications in hybrids, as mismatches between maternal pelvic and fetal cranial morphology are often fatal to mother and offspring. As the pelvis is also one of the skeletal regions that differs most between Homo sapiens and Neanderthals, investigating the pelvic consequences of interbreeding could be informative regarding the viability of their hybrids. We find that the effect of admixture in M. mulatta is small and proportional to the relatively small morphological difference between the parent taxa. Sexual dimorphism appears to be the main determinant of pelvic shape in M. mulatta. The lack of difference in pelvic shape between Chinese and Indian M. mulatta is in contrast to that between Neanderthals and H. sapiens, despite a similar split time (in generations) between the hybridizing pairs. Greater phenotypic divergence between hominins may relate to adaptations to disparate environments but may also highlight how the unique degree of cultural buffering in hominins allowed for greater neutral divergence. In contrast to some previous work identifying extreme morphologies in first- and second-generation hybrids, here the relationship between pelvic shape and admixture is linear. This linearity may be because most sampled animals have a multigenerational admixture history or because of relatively high constraints on the pelvis compared with other skeletal regions.}, }
@article {pmid34437543, year = {2021}, author = {Heydari-Guran, S and Benazzi, S and Talamo, S and Ghasidian, E and Hariri, N and Oxilia, G and Asiabani, S and Azizi, F and Naderi, R and Safaierad, R and Hublin, JJ and Foley, RA and Lahr, MM}, title = {The discovery of an in situ Neanderthal remain in the Bawa Yawan Rockshelter, West-Central Zagros Mountains, Kermanshah.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0253708}, pmid = {34437543}, issn = {1932-6203}, mesh = {Animals ; Body Remains/anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; History, Ancient ; Iran ; Neanderthals/*anatomy &amp; histology ; Tooth/anatomy &amp; histology ; }, abstract = {Neanderthal extinction has been a matter of debate for many years. New discoveries, better chronologies and genomic evidence have done much to clarify some of the issues. This evidence suggests that Neanderthals became extinct around 40,000-37,000 years before present (BP), after a period of coexistence with Homo sapiens of several millennia, involving biological and cultural interactions between the two groups. However, the bulk of this evidence relates to Western Eurasia, and recent work in Central Asia and Siberia has shown that there is considerable local variation. Southwestern Asia, despite having a number of significant Neanderthal remains, has not played a major part in the debate over extinction. Here we report a Neanderthal deciduous canine from the site of Bawa Yawan in the West-Central Zagros Mountains of Iran. The tooth is associated with Zagros Mousterian lithics, and its context is preliminary dated to between ~43,600 and ~41,500 years ago.}, }
@article {pmid34433829, year = {2021}, author = {Hsieh, P and Dang, V and Vollger, MR and Mao, Y and Huang, TH and Dishuck, PC and Baker, C and Cantsilieris, S and Lewis, AP and Munson, KM and Sorensen, M and Welch, AE and Underwood, JG and Eichler, EE}, title = {Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5118}, pmid = {34433829}, issn = {2041-1723}, support = {K99 HG011041/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; DNA Copy Number Variations ; Evolution, Molecular ; *Gene Duplication ; Genome, Human ; Haplotypes ; Hominidae/*genetics ; Humans ; Membrane Proteins/*genetics ; Neanderthals ; Phylogeny ; *Selection, Genetic ; }, abstract = {TRP channel-associated factor 1/2 (TCAF1/TCAF2) proteins antagonistically regulate the cold-sensor protein TRPM8 in multiple human tissues. Understanding their significance has been complicated given the locus spans a gap-ridden region with complex segmental duplications in GRCh38. Using long-read sequencing, we sequence-resolve the locus, annotate full-length TCAF models in primate genomes, and show substantial human-specific TCAF copy number variation. We identify two human super haplogroups, H4 and H5, and establish that TCAF duplications originated ~1.7 million years ago but diversified only in Homo sapiens by recurrent structural mutations. Conversely, in all archaic-hominin samples the fixation for a specific H4 haplotype without duplication is likely due to positive selection. Here, our results of TCAF copy number expansion, selection signals in hominins, and differential TCAF2 expression between haplogroups and high TCAF2 and TRPM8 expression in liver and prostate in modern-day humans imply TCAF diversification among hominins potentially in response to cold or dietary adaptations.}, }
@article {pmid34428206, year = {2021}, author = {Richards, MP and Mannino, MA and Jaouen, K and Dozio, A and Hublin, JJ and Peresani, M}, title = {Strontium isotope evidence for Neanderthal and modern human mobility at the upper and middle palaeolithic site of Fumane Cave (Italy).}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0254848}, pmid = {34428206}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; *Caves ; Dental Enamel/chemistry ; Geography ; Hominidae ; Humans ; Italy ; Neanderthals/*physiology ; Strontium Isotopes/*analysis ; Time Factors ; Tooth/chemistry ; }, abstract = {To investigate the mobility patterns of Neanderthals and modern humans in Europe during the Middle-to-Upper Palaeolithic transition period, we applied strontium isotope analysis to Neanderthal (n = 3) and modern human (n = 2) teeth recovered from the site of Fumane Cave in the Monti Lessini region of Northern Italy. We also measured a large number of environmental samples from the region, to establish a strontium 'baseline', and also micromammals (vole teeth) from the levels associated with the hominin teeth. We found that the modern humans and Neanderthals had similar strontium isotope values, and these values match the local baseline values we obtained for the site and the surrounding region. We conclude that both groups were utilizing the local mountainous region where Fumane Cave is situated, and likely the nearby Lessini highlands and Adige plains, and therefore the strontium evidence does not show differening mobility patterns between Neanderthals and modern humans at the Fumane site.}, }
@article {pmid34413328, year = {2021}, author = {Bensusan, K and Holmes, TL and Perez, C and Finlayson, G and Finlayson, S and Guillem, R and Finlayson, C}, title = {Crag Martin neontology complements taphonomy at the Gorham's Cave Complex.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {16851}, pmid = {34413328}, issn = {2045-2322}, abstract = {Species present in the fossil record may continue to exist at an archaeological site, allowing study that fine-tunes our picture of the ecological past. A large wintering population of Eurasian Crag Martins Ptyonoprogne rupestris (ECM) roosts at the 'Gorham's Cave Complex' UNESCO World Heritage site in Gibraltar, which is best known for its occupation by Neanderthals at times when ECMs were also present. Its complex geomorphology allows the study of use of different micro-sites (caves) within the roost. We used mark-recapture to test whether birds showed fidelity to micro-sites for roosting, and for differences in condition of birds across micro-sites. ECM showed very high fidelity towards micro-sites, within and between years, with > 90% chance of recapture at caves where they were first caught. Condition of birds differed between micro-sites, suggesting differences in roost quality between caves; birds were more likely to be recaptured at the micro-site where birds were in best condition, indicating higher survivorship. Our results demonstrate extremely fine-scale fidelity at the largest roosting site documented for ECM globally. Implications for conservation are discussed. The study provides current knowledge of a bird that has been using these caves since the Pleistocene and more generally on these caves as refuges.}, }
@article {pmid34403991, year = {2021}, author = {Estalrrich, A and Marín-Arroyo, AB}, title = {Evidence of habitual behavior from non-alimentary dental wear on deciduous teeth from the Middle and Upper Paleolithic Cantabrian region, Northern Spain.}, journal = {Journal of human evolution}, volume = {158}, number = {}, pages = {103047}, doi = {10.1016/j.jhevol.2021.103047}, pmid = {34403991}, issn = {1095-8606}, mesh = {Animals ; *Fossils ; History, Ancient ; Humans ; *Neanderthals ; Paleodontology ; Spain ; *Tooth Wear ; Tooth, Deciduous/*anatomy &amp; histology ; }, abstract = {The use of 'teeth as tools' (non-masticatory or cultural-related dental wear) has largely been employed as a proxy for studying of past human behavior, mainly in permanent dentition from adult individuals. Here we present the analysis of the non-masticatory dental wear modifications on the deciduous dentition assigned to eight Neanderthal and anatomically modern human subadult individuals from Mousterian to Magdalenian technocultural contexts in the Cantabrian region (Northern Spain). Although preliminary, we tentatively suggest that these eight subadults present activity-related dental wear, including cultural striations, chipped enamel, toothpick grooves, and subvertical grooves. We also found evidence of habitual dental hygienic practices in the form of toothpicking on a deciduous premolar. Orientation of the cultural striations indicates similar handedness development as in modern children. Taken together, these dental wear patterns support the participation of young individuals in group activities, making them potential contributors to group welfare. This study potentially adds new evidence to the importance of the use of the mouth in paramasticatory activities or as a third hand throughout the Pleistocene, which can be confirmed with a more specific reference sample.}, }
@article {pmid34388371, year = {2021}, author = {Larena, M and McKenna, J and Sanchez-Quinto, F and Bernhardsson, C and Ebeo, C and Reyes, R and Casel, O and Huang, JY and Hagada, KP and Guilay, D and Reyes, J and Allian, FP and Mori, V and Azarcon, LS and Manera, A and Terando, C and Jamero, L and Sireg, G and Manginsay-Tremedal, R and Labos, MS and Vilar, RD and Latiph, A and Saway, RL and Marte, E and Magbanua, P and Morales, A and Java, I and Reveche, R and Barrios, B and Burton, E and Salon, JC and Kels, MJT and Albano, A and Cruz-Angeles, RB and Molanida, E and Granehäll, L and Vicente, M and Edlund, H and Loo, JH and Trejaut, J and Ho, SYW and Reid, L and Lambeck, K and Malmström, H and Schlebusch, C and Endicott, P and Jakobsson, M}, title = {Philippine Ayta possess the highest level of Denisovan ancestry in the world.}, journal = {Current biology : CB}, volume = {31}, number = {19}, pages = {4219-4230.e10}, pmid = {34388371}, issn = {1879-0445}, mesh = {Animals ; Asia ; Asia, Southeastern ; Australia ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Philippines ; Racial Groups ; }, abstract = {Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world-∼30%-40% greater than that of Australians and Papuans-consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.}, }
@article {pmid34386877, year = {2021}, author = {Paar, V and Vlahović, I and Rosandić, M and Glunčić, M}, title = {Global Repeat Map (GRM): Advantageous Method for Discovery of Largest Higher-Order Repeats (HORs) in Neuroblastoma Breakpoint Family (NBPF) Genes, in Hornerin Exon and in Chromosome 21 Centromere.}, journal = {Progress in molecular and subcellular biology}, volume = {60}, number = {}, pages = {203-234}, pmid = {34386877}, issn = {0079-6484}, mesh = {Animals ; Centromere ; *Chromosomes, Human, Pair 21 ; DNA, Satellite ; Exons ; Genome, Human/genetics ; Humans ; *Neuroblastoma/genetics ; }, abstract = {Here we present three interesting novel human Higher-Order Repeats (HORs) discovered using the HOR-searching method with GRM algorithm: (a) The novel Neuroblastoma Breakpoint Family gene (NBPF) 3mer HOR, discovered applying GRM algorithm to human chromosome 1 (Paar et al., Mol Biol Evol 28:1877-1892, 2011). NBPF 3mer HOR is based on previously known ~1.6 kb NBPF primary repeat monomers (known as DUF1220 domain) in human chromosome 1, but the NBPF HOR was not known before its discovery by using GRM. It should be stressed that the NBPF HOR presents a unique human-specific pattern, distinguishing human from nonhuman primates. (b) The novel quartic HOR (2mer⊃2mer⊃9mer) discovered using the GRM algorithm for analysis of hornerin genes in human chromosome 1 (Paar et al., Mol Biol Evol 28:1877-1892, 2011). This quartic HOR is based on 39 bp hornerin primary repeat monomer in human chromosome 1. To our knowledge, this is the first known case of quartic HOR, with four levels of hierarchy of HOR organization. (c) The novel 33mer alpha satellite HOR in human chromosome 21, discovered using the GRM algorithm (Glunčić et al., Sci Rep 9:12629, 2019). This 33mer HOR in the smallest human chromosome is the largest alpha satellite HOR copy among all 22 somatic human chromosomes. Moreover, the same 33mer HOR is present in the hg38 human genome assembly of four human chromosomes: 21, 22, 13, and 14. We point out that the DUF1220 encoding genomic structures in NBPF genes in human chromosome 1, recently studied and related to the brain evolution and pathologies and cognitive aptitude, can be considered in the framework of the general concept of HORs, already extensively studied in genomics, especially in the centromeric region.}, }
@article {pmid34352227, year = {2021}, author = {Almarri, MA and Haber, M and Lootah, RA and Hallast, P and Al Turki, S and Martin, HC and Xue, Y and Tyler-Smith, C}, title = {The genomic history of the Middle East.}, journal = {Cell}, volume = {184}, number = {18}, pages = {4612-4625.e14}, pmid = {34352227}, issn = {1097-4172}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Chromosomes, Human, Y/genetics ; Databases, Genetic ; Gene Pool ; Genetic Introgression ; Genetics, Population/*history ; *Genome, Human ; Geography ; History, Ancient ; Human Migration ; Humans ; Middle East ; Models, Genetic ; Neanderthals/genetics ; Phylogeny ; Population Density ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {The Middle East region is important to understand human evolution and migrations but is underrepresented in genomic studies. Here, we generated 137 high-coverage physically phased genome sequences from eight Middle Eastern populations using linked-read sequencing. We found no genetic traces of early expansions out-of-Africa in present-day populations but found Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. Population sizes within the region started diverging 15-20 kya, when Levantines expanded while Arabians maintained smaller populations that derived ancestry from local hunter-gatherers. Arabians suffered a population bottleneck around the aridification of Arabia 6 kya, while Levantines had a distinct bottleneck overlapping the 4.2 kya aridification event. We found an association between movement and admixture of populations in the region and the spread of Semitic languages. Finally, we identify variants that show evidence of selection, including polygenic selection. Our results provide detailed insights into the genomic and selective histories of the Middle East.}, }
@article {pmid34350666, year = {2021}, author = {Madison, P}, title = {Brutish Neanderthals: History of a merciless characterization.}, journal = {Evolutionary anthropology}, volume = {30}, number = {6}, pages = {366-374}, doi = {10.1002/evan.21918}, pmid = {34350666}, issn = {1520-6505}, mesh = {Animals ; Humans ; *Neanderthals ; }, abstract = {The idea that Neanderthals were brutish and unintelligent is often traced back to Marcellin Boule, a French paleontologist who examined the specimen known as the Old Man in the first decades of the 20th century. This article examines the work of Boule's predecessors and aggregate a variety of literature to underline an argument that this idea has much earlier origins and is rooted in the first recognized specimen discovered in the Neander Valley in 1856. Reorienting our understanding of the brutish Neanderthal to account for its 19th-century origins, allows for a reexamination of the factors in 19th-century culture, science, and society which contributed to this caricature, especially the concepts of race and species' extinction. Such a reexamination dismantles the narrative of Boule's error while providing a new vantage point to think about Neanderthals in the present.}, }
@article {pmid34341069, year = {2021}, author = {Pitarch Martí, A and Zilhão, J and d'Errico, F and Cantalejo-Duarte, P and Domínguez-Bella, S and Fullola, JM and Weniger, GC and Ramos-Muñoz, J}, title = {The symbolic role of the underground world among Middle Paleolithic Neanderthals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {33}, pages = {}, pmid = {34341069}, issn = {1091-6490}, abstract = {Cueva de Ardales in Málaga, Spain, is one of the richest and best-preserved Paleolithic painted caves of southwestern Europe, containing over a thousand graphic representations. Here, we study the red pigment in panel II.A.3 of "Sala de las Estrellas," dated by U-Th to the Middle Paleolithic, to determine its composition, verify its anthropogenic nature, infer the associated behaviors, and discuss their implications. Using optical microscopy, scanning electron microscopy coupled with energy dispersive X-ray spectroscopy, micro-Raman spectroscopy, and X-ray diffraction, we analyzed a set of samples from the panel and compared them to natural coloring materials collected from the floor and walls of the cave. The conspicuously different texture and composition of the geological samples indicates that the pigments used in the paintings do not come from the outcrops of colorant material known in the cave. We confirm that the paintings are not the result of natural processes and show that the composition of the paint is consistent with the artistic activity being recurrent. Our results strengthen the hypothesis that Neanderthals symbolically used these paintings and the large stalagmitic dome harboring them over an extended time span.}, }
@article {pmid34340120, year = {2021}, author = {Bowland, LA and Scott, JE and Kivell, TL and Patel, BA and Tocheri, MW and Orr, CM}, title = {Homo naledi pollical metacarpal shaft morphology is distinctive and intermediate between that of australopiths and other members of the genus Homo.}, journal = {Journal of human evolution}, volume = {158}, number = {}, pages = {103048}, doi = {10.1016/j.jhevol.2021.103048}, pmid = {34340120}, issn = {1095-8606}, support = {P40 OD012217/OD/NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Caves ; *Fossils ; Haplorhini/anatomy &amp; histology ; Hominidae/*anatomy &amp; histology ; Humans ; Metacarpal Bones/*anatomy &amp; histology ; Neanderthals/anatomy &amp; histology ; }, abstract = {Homo naledi fossils from the Rising Star cave system provide important insights into the diversity of hand morphology within the genus Homo. Notably, the pollical (thumb) metacarpal (Mc1) displays an unusual suite of characteristics including a median longitudinal crest, a narrow proximal base, and broad flaring intrinsic muscle flanges. The present study evaluates the affinities of H. naledi Mc1 morphology via 3D geometric morphometric analysis of shaft shape using a broader comparative sample (n = 337) of fossil hominins, recent humans, apes, and cercopithecoid monkeys than in prior work. Results confirm that the H. naledi Mc1 is distinctive from most other hominins in being narrow at the proximal end but surmounted by flaring muscle flanges distally. Only StW 418 (Australopithecus cf. africanus) is similar in these aspects of shape. The gracile proximal shaft is most similar to cercopithecoids, Pan, Pongo, Australopithecus afarensis, and Australopithecus sediba, suggesting that H. naledi retains the condition primitive for the genus Homo. In contrast, Neandertal Mc1s are characterized by wide proximal bases and shafts, pinched midshafts, and broad distal flanges, while those of recent humans generally have straight shafts, less robust muscle flanges, and wide proximal shafts/bases. Although uncertainties remain regarding character polarity, the morphology of the H. naledi thumb might be interpreted as a retained intermediate state in a transformation series between the overall gracility of the shaft and the robust shafts of later hominins. Such a model suggests that the addition of broad medial and lateral muscle flanges to a primitively slender shaft was the first modification in transforming the Mc1 into the overall more robust structure exhibited by other Homo taxa including Neandertals and recent Homo sapiens in whose shared lineage the bases and proximal shafts became expanded, possibly as an adaptation to the repeated recruitment of powerful intrinsic pollical muscles.}, }
@article {pmid34335974, year = {2021}, author = {Zhang, Q and Wadgaonkar, P and Xu, L and Thakur, C and Fu, Y and Bi, Z and Qiu, Y and Almutairy, B and Zhang, W and Stemmer, P and Chen, F}, title = {Environmentally-induced mdig contributes to the severity of COVID-19 through fostering expression of SARS-CoV-2 receptor NRPs and glycan metabolism.}, journal = {Theranostics}, volume = {11}, number = {16}, pages = {7970-7983}, pmid = {34335974}, issn = {1838-7640}, support = {R01 ES028263/ES/NIEHS NIH HHS/United States ; R01 ES028335/ES/NIEHS NIH HHS/United States ; R01 ES031822/ES/NIEHS NIH HHS/United States ; }, mesh = {Alveolar Epithelial Cells/metabolism ; Animals ; COVID-19/epidemiology/*metabolism/*virology ; Cathepsins/metabolism ; Cell Line ; Cells, Cultured ; Dioxygenases/biosynthesis/genetics/*metabolism ; Environmental Exposure ; Histone Demethylases/biosynthesis/genetics/*metabolism ; Histones/metabolism ; Humans ; Neuropilin-1/*metabolism ; Nuclear Proteins/biosynthesis/genetics/*metabolism ; Pandemics ; Polysaccharides/*metabolism ; Rats ; SARS-CoV-2/*metabolism/pathogenicity ; Spike Glycoprotein, Coronavirus/metabolism ; }, abstract = {The novel β-coronavirus, SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19), has infected more than 177 million people and resulted in 3.84 million death worldwide. Recent epidemiological studies suggested that some environmental factors, such as air pollution, might be the important contributors to the mortality of COVID-19. However, how environmental exposure enhances the severity of COVID-19 remains to be fully understood. In the present report, we provided evidence showing that mdig, a previously reported environmentally-induced oncogene that antagonizes repressive trimethylation of histone proteins, is an important regulator for SARS-CoV-2 receptors neuropilin-1 (NRP1) and NRP2, cathepsins, glycan metabolism and inflammation, key determinants for viral infection and cytokine storm of the patients. Depletion of mdig in bronchial epithelial cells by CRISPR-Cas-9 gene editing resulted in a decreased expression of NRP1, NRP2, cathepsins, and genes involved in protein glycosylation and inflammation, largely due to a substantial enrichment of lysine 9 and/or lysine 27 trimethylation of histone H3 (H3K9me3/H3K27me3) on these genes as determined by ChIP-seq. Meanwhile, we also validated that environmental factor arsenic is able to induce mdig, NRP1 and NRP2, and genetic disruption of mdig lowered expression of NRP1 and NRP2. Furthermore, mdig may coordinate with the Neanderthal variants linked to an elevated mortality of COVID-19. These data, thus, suggest that mdig is a key mediator for the severity of COVID-19 in response to environmental exposure and targeting mdig may be the one of the effective strategies in ameliorating the symptom and reducing the mortality of COVID-19.}, }
@article {pmid34320013, year = {2021}, author = {Condemi, S and Mazières, S and Faux, P and Costedoat, C and Ruiz-Linares, A and Bailly, P and Chiaroni, J}, title = {Blood groups of Neandertals and Denisova decrypted.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0254175}, pmid = {34320013}, issn = {1932-6203}, mesh = {Alleles ; Animals ; Blood Group Antigens/*genetics ; Fossils ; Genetic Variation ; Genotype ; Hominidae/*genetics ; INDEL Mutation ; Neanderthals/*genetics ; Phenotype ; Polymorphism, Genetic ; }, abstract = {Blood group systems were the first phenotypic markers used in anthropology to decipher the origin of populations, their migratory movements, and their admixture. The recent emergence of new technologies based on the decoding of nucleic acids from an individual's entire genome has relegated them to their primary application, blood transfusion. Thus, despite the finer mapping of the modern human genome in relation to Neanderthal and Denisova populations, little is known about red cell blood groups in these archaic populations. Here we analyze the available high-quality sequences of three Neanderthals and one Denisovan individuals for 7 blood group systems that are used today in transfusion (ABO including H/Se, Rh (Rhesus), Kell, Duffy, Kidd, MNS, Diego). We show that Neanderthal and Denisova were polymorphic for ABO and shared blood group alleles recurrent in modern Sub-Saharan populations. Furthermore, we found ABO-related alleles currently preventing from viral gut infection and Neanderthal RHD and RHCE alleles nowadays associated with a high risk of hemolytic disease of the fetus and newborn. Such a common blood group pattern across time and space is coherent with a Neanderthal population of low genetic diversity exposed to low reproductive success and with their inevitable demise. Lastly, we connect a Neanderthal RHD allele to two present-day Aboriginal Australian and Papuan, suggesting that a segment of archaic genome was introgressed in this gene in non-Eurasian populations. While contributing to both the origin and late evolutionary history of Neanderthal and Denisova, our results further illustrate that blood group systems are a relevant piece of the puzzle helping to decipher it.}, }
@article {pmid34312431, year = {2021}, author = {Alcaraz-Castaño, M and Alcolea-González, JJ and de Andrés-Herrero, M and Castillo-Jiménez, S and Cuartero, F and Cuenca-Bescós, G and Kehl, M and López-Sáez, JA and Luque, L and Pérez-Díaz, S and Piqué, R and Ruiz-Alonso, M and Weniger, GC and Yravedra, J}, title = {First modern human settlement recorded in the Iberian hinterland occurred during Heinrich Stadial 2 within harsh environmental conditions.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15161}, pmid = {34312431}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Bayes Theorem ; Charcoal/history ; Climate ; Environment ; Fossils/history ; Geologic Sediments/analysis ; Geological Phenomena ; History, Ancient ; Human Migration/*history ; Humans ; Models, Biological ; Pollen/chemistry ; Population Dynamics/history ; Radiometric Dating ; Spain ; Vertebrates ; Wood/history ; }, abstract = {As the south-westernmost region of Europe, the Iberian Peninsula stands as a key area for understanding the process of modern human dispersal into Eurasia. However, the precise timing, ecological setting and cultural context of this process remains controversial concerning its spatiotemporal distribution within the different regions of the peninsula. While traditional models assumed that the whole Iberian hinterland was avoided by modern humans due to ecological factors until the retreat of the Last Glacial Maximum, recent research has demonstrated that hunter-gatherers entered the Iberian interior at least during Solutrean times. We provide a multi-proxy geoarchaeological, chronometric and paleoecological study on human-environment interactions based on the key site of Peña Capón (Guadalajara, Spain). Results show (1) that this site hosts the oldest modern human presence recorded to date in central Iberia, associated to pre-Solutrean cultural traditions around 26,000 years ago, and (2) that this presence occurred during Heinrich Stadial 2 within harsh environmental conditions. These findings demonstrate that this area of the Iberian hinterland was recurrently occupied regardless of climate and environmental variability, thus challenging the widely accepted hypothesis that ecological risk hampered the human settlement of the Iberian interior highlands since the first arrival of modern humans to Southwest Europe.}, }
@article {pmid34294692, year = {2021}, author = {McArthur, E and Rinker, DC and Capra, JA}, title = {Quantifying the contribution of Neanderthal introgression to the heritability of complex traits.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4481}, pmid = {34294692}, issn = {2041-1723}, support = {F30 HG011200/HG/NHGRI NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Alleles ; Animals ; Cognition ; Female ; *Genetic Introgression ; Genetic Variation ; Genome, Human ; Genome-Wide Association Study ; Hair/anatomy &amp; histology ; Humans ; Linkage Disequilibrium ; Male ; *Models, Genetic ; *Multifactorial Inheritance ; Neanderthals/anatomy &amp; histology/*genetics/physiology ; Phenotype ; Selection, Genetic ; }, abstract = {Eurasians have ~2% Neanderthal ancestry, but we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human diseases and traits. Here, we quantify the contribution of introgressed alleles to the heritability of more than 400 diverse traits. We show that genomic regions in which detectable Neanderthal ancestry remains are depleted of heritability for all traits considered, except those related to skin and hair. Introgressed variants themselves are also depleted for contributions to the heritability of most traits. However, introgressed variants shared across multiple Neanderthal populations are enriched for heritability and have consistent directions of effect on several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. Integrating our results, we propose a model in which selection against introgressed functional variation was the dominant trend (especially for cognitive traits); however, for a few traits, introgressed variants provided beneficial variation via uni-directional (e.g., lightening skin color) or bi-directional (e.g., modulating immune response) effects.}, }
@article {pmid34285394, year = {2021}, author = {Leder, D and Hermann, R and Hüls, M and Russo, G and Hoelzmann, P and Nielbock, R and Böhner, U and Lehmann, J and Meier, M and Schwalb, A and Tröller-Reimer, A and Koddenberg, T and Terberger, T}, title = {Publisher Correction: A 51,000-year-old engraved bone reveals Neanderthals' capacity for symbolic behaviour.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {9}, pages = {1320}, doi = {10.1038/s41559-021-01537-6}, pmid = {34285394}, issn = {2397-334X}, }
@article {pmid34282422, year = {2021}, author = {Banday, AR and Stanifer, ML and Florez-Vargas, O and Onabajo, OO and Zahoor, MA and Papenberg, BW and Ring, TJ and Lee, CH and Andreakos, E and Arons, E and Barsh, G and Biesecker, LG and Boyle, DL and Burnett-Hartman, A and Carrington, M and Chang, E and Choe, PG and Chrisholm, RL and Dalgard, C and Edberg, J and Erdmann, N and Feigelson, HS and Firestein, GS and Gehring, AJ and Ho, M and Holland, S and Hutchinson, AA and Im, H and Ison, MG and Kim, HB and Kreitman, RJ and Korf, BR and Mirabello, L and Pacheco, JA and Peluso, MJ and Rader, DJ and Redden, DT and Ritchie, MD and Rosenbloom, B and Sant Anna, HP and Savage, S and Siouti, E and Triantafyllia, V and Vargas, JM and Verma, A and Vij, V and Wesemann, DR and Yeager, M and Yu, X and Zhang, Y and Boulant, S and Chanock, SJ and Feld, JJ and Prokunina-Olsson, L}, title = {Genetic regulation of OAS1 nonsense-mediated decay underlies association with risk of severe COVID-19.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {34282422}, support = {U01 AI148108/AI/NIAID NIH HHS/United States ; UL1 TR003096/TR/NCATS NIH HHS/United States ; }, abstract = {Genomic regions have been associated with COVID-19 susceptibility and outcomes, including the chr12q24.13 locus encoding antiviral proteins OAS1-3. Here, we report genetic, functional, and clinical insights into genetic associations within this locus. In Europeans, the risk of hospitalized vs. non-hospitalized COVID-19 was associated with a single 19Kb-haplotype comprised of 76 OAS1 variants included in a 95% credible set within a large genomic fragment introgressed from Neandertals. The risk haplotype was also associated with impaired spontaneous but not treatment-induced SARS-CoV-2 clearance in a clinical trial with pegIFN-λ1. We demonstrate that two exonic variants, rs10774671 and rs1131454, affect splicing and nonsense-mediated decay of OAS1 . We suggest that genetically-regulated loss of OAS1 expression contributes to impaired spontaneous clearance of SARS-CoV-2 and elevated risk of hospitalization for COVID-19. Our results provide the rationale for further clinical studies using interferons to compensate for impaired spontaneous SARS-CoV-2 clearance, particularly in carriers of the OAS1 risk haplotypes.}, }
@article {pmid34272242, year = {2021}, author = {Schaefer, NK and Shapiro, B and Green, RE}, title = {An ancestral recombination graph of human, Neanderthal, and Denisovan genomes.}, journal = {Science advances}, volume = {7}, number = {29}, pages = {}, pmid = {34272242}, issn = {2375-2548}, support = {T32 HG008345/HG/NHGRI NIH HHS/United States ; T32 HG00834/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Genome, Human ; Genomics ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Recombination, Genetic ; }, abstract = {Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function.}, }
@article {pmid34254144, year = {2021}, author = {Iasi, LNM and Ringbauer, H and Peter, BM}, title = {An Extended Admixture Pulse Model Reveals the Limitations to Human-Neandertal Introgression Dating.}, journal = {Molecular biology and evolution}, volume = {38}, number = {11}, pages = {5156-5174}, pmid = {34254144}, issn = {1537-1719}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; DNA/genetics ; Gene Flow ; Genome ; Humans ; *Neanderthals/genetics ; }, abstract = {Neandertal DNA makes up 2-3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended admixture pulse model that allows joint estimation of the timing and duration of gene flow. This model leads to simple expressions for both the admixture segment distribution and the decay curve of ancestry linkage disequilibrium, and we show that these two statistics are closely related. In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models, but that the duration of the gene flow can only be recovered if gene flow is very recent and the exact recombination map is known. These results imply that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted.}, }
@article {pmid34226702, year = {2021}, author = {Leder, D and Hermann, R and Hüls, M and Russo, G and Hoelzmann, P and Nielbock, R and Böhner, U and Lehmann, J and Meier, M and Schwalb, A and Tröller-Reimer, A and Koddenberg, T and Terberger, T}, title = {A 51,000-year-old engraved bone reveals Neanderthals' capacity for symbolic behaviour.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {9}, pages = {1273-1282}, pmid = {34226702}, issn = {2397-334X}, mesh = {Animals ; Bone and Bones ; Caves ; *Deer ; Europe ; Humans ; Infant, Newborn ; *Neanderthals ; }, abstract = {While there is substantial evidence for art and symbolic behaviour in early Homo sapiens across Africa and Eurasia, similar evidence connected to Neanderthals is sparse and often contested in scientific debates. Each new discovery is thus crucial for our understanding of Neanderthals' cognitive capacity. Here we report on the discovery of an at least 51,000-year-old engraved giant deer phalanx found at the former cave entrance of Einhornhöhle, northern Germany. The find comes from an apparent Middle Palaeolithic context that is linked to Neanderthals. The engraved bone demonstrates that conceptual imagination, as a prerequisite to compose individual lines into a coherent design, was present in Neanderthals. Therefore, Neanderthal's awareness of symbolic meaning is very likely. Our findings show that Neanderthals were capable of creating symbolic expressions before H. sapiens arrived in Central Europe.}, }
@article {pmid34226701, year = {2021}, author = {Bello, SM}, title = {Boning up on Neanderthal art.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {9}, pages = {1201-1202}, pmid = {34226701}, issn = {2397-334X}, mesh = {Animals ; Meat/analysis ; *Neanderthals ; }, }
@article {pmid34214909, year = {2021}, author = {Bergmann, I and Hublin, JJ and Gunz, P and Freidline, SE}, title = {How did modern morphology evolve in the human mandible? The relationship between static adult allometry and mandibular variability in Homo sapiens.}, journal = {Journal of human evolution}, volume = {157}, number = {}, pages = {103026}, doi = {10.1016/j.jhevol.2021.103026}, pmid = {34214909}, issn = {1095-8606}, mesh = {Adult ; Animals ; Female ; *Fossils ; Humans ; Male ; Mandible/*anatomy &amp; histology ; Neanderthals/anatomy &amp; histology ; }, abstract = {Key to understanding human origins are early Homo sapiens fossils from Jebel Irhoud, as well as from the early Late Pleistocene sites Tabun, Border Cave, Klasies River Mouth, Skhul, and Qafzeh. While their upper facial shape falls within the recent human range of variation, their mandibles display a mosaic morphology. Here we quantify how mandibular shape covaries with mandible size and how static allometry differs between Neanderthals, early H. sapiens, and modern humans from the Upper Paleolithic/Later Stone Age and Holocene (= later H. sapiens). We use 3D (semi)landmark geometric morphometric methods to visualize allometric trends and to explore how gracilization affects the expression of diagnostic shape features. Early H. sapiens were highly variable in mandible size, exhibiting a unique allometric trajectory that explains aspects of their 'archaic' appearance. At the same time, early H. sapiens share a suite of diagnostic features with later H. sapiens that are not related to mandibular sizes, such as an incipient chin and an anteroposteriorly decreasing corpus height. The mandibular morphology, often referred to as 'modern', can partly be explained by gracilization owing to size reduction. Despite distinct static allometric shape changes in each group studied, bicondylar and bigonial breadth represent important structural constraints for the expression of shape features in most Middle to Late Pleistocene hominin mandibles.}, }
@article {pmid34166582, year = {2022}, author = {Schwartz, JH and Pantoja-Pérez, A and Arsuaga, JL}, title = {The nasal region of the ~417 ka Sima de los Huesos (Sierra de Atapuerca, Spain) Hominin: New terminology and implications for later human evolution.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {305}, number = {8}, pages = {1991-2029}, doi = {10.1002/ar.24698}, pmid = {34166582}, issn = {1932-8494}, mesh = {Animals ; Biological Evolution ; Fossils ; *Hominidae/anatomy &amp; histology ; Humans ; Mammals ; *Neanderthals/anatomy &amp; histology ; Phylogeny ; Spain ; }, abstract = {Circum-nasal and nasal cavity morphology add to the picture of the Sima de los Huesos specimens as, at one level, representing a distinct morph and, at another, displaying individual variation. They developed a robust, midline-grooved, three-dimensional spinal ridge lying anteriorly in the nasal cavity floor that was distended posteriorly over the nasal cavity floor, and, typically, an expansive, three-dimensional patch of rugose bone on the nasal cavity wall where a conchal crest would otherwise lie. They vary, for example, in degree of topographic relief of the nasal cavity wall, expression of the spinal ridge, and development of nasal crests and fossae. Lacking an anterior nasal spine, Sima specimens differ from extant and most fossil Homo sapiens, some specimens attributed to H. heidelbergensis, and the Gran Dolina partial face, whose anterior nasal spine is a superoanterior distention of the nasoalveolar clivus, and also from Neanderthals, whose anterior nasal spine projects anteriorly away from the nasoalveolar clivus. Comparison of Neanderthals, the Sima hominin, and specimens regarded as H. heidelbergensis calls for re-evaluating the integrity of "heidelbergensis" and rethinking the phylogenetic relationships of them all. To precisely describe the numerous features and combinations thereof of the nasal region in Sima specimens, and compare them with Neandertals and "H. heidelbergensis", we developed terminology that is applicable not only to hominins, but to mammals in general.}, }
@article {pmid34163072, year = {2021}, author = {Zavala, EI and Jacobs, Z and Vernot, B and Shunkov, MV and Kozlikin, MB and Derevianko, AP and Essel, E and de Fillipo, C and Nagel, S and Richter, J and Romagné, F and Schmidt, A and Li, B and O'Gorman, K and Slon, V and Kelso, J and Pääbo, S and Roberts, RG and Meyer, M}, title = {Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave.}, journal = {Nature}, volume = {595}, number = {7867}, pages = {399-403}, pmid = {34163072}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; }, mesh = {Animals ; Archaeology ; *Caves ; DNA, Ancient/*analysis ; DNA, Mitochondrial/analysis/genetics ; Fossils ; Geologic Sediments/*chemistry ; History, Ancient ; Hominidae/*genetics ; Neanderthals/genetics ; Siberia ; }, abstract = {Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals[1-4]. The dozen hominin remains recovered from the deposits also include Neanderthals[5,6] and the child of a Neanderthal and a Denisovan[7], which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages[5,8-11]. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly-possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.}, }
@article {pmid34158647, year = {2021}, author = {Curry, A}, title = {How ancient people fell in love with bread, beer and other carbs.}, journal = {Nature}, volume = {594}, number = {7864}, pages = {488-491}, pmid = {34158647}, issn = {1476-4687}, mesh = {Agriculture/history ; Animals ; *Archaeology ; Austria ; Beer/*history ; Bread/*history ; Dental Plaque/chemistry/microbiology ; Diet/*history ; Diet, Paleolithic ; Dietary Carbohydrates ; Edible Grain/*history ; Feces/chemistry ; History, Ancient ; Humans ; Meat/history ; Neanderthals ; Netherlands ; Turkey ; Vegetables/history ; Vegetarians/history ; }, }
@article {pmid34155120, year = {2021}, author = {Devièse, T and Abrams, G and Hajdinjak, M and Pirson, S and De Groote, I and Di Modica, K and Toussaint, M and Fischer, V and Comeskey, D and Spindler, L and Meyer, M and Semal, P and Higham, T}, title = {Reply to Van Peer: Direct radiocarbon dating and ancient genomic analysis reveal the true age of the Neanderthals at Spy Cave.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {26}, pages = {}, pmid = {34155120}, issn = {1091-6490}, mesh = {Animals ; Caves ; Fossils ; Genomics ; *Neanderthals/genetics ; Radiometric Dating ; }, }
@article {pmid34155119, year = {2021}, author = {Van Peer, P}, title = {The stratigraphic context of Spy Cave and the timing of Neanderthal disappearance in Northwest Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {26}, pages = {}, pmid = {34155119}, issn = {1091-6490}, mesh = {Animals ; Caves ; Europe ; *Neanderthals ; Radiometric Dating ; }, }
@article {pmid34150310, year = {2021}, author = {Amos, W}, title = {Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding.}, journal = {Royal Society open science}, volume = {8}, number = {6}, pages = {201229}, pmid = {34150310}, issn = {2054-5703}, abstract = {Although the presence of archaic hominin legacies in humans is taken for granted, little attention has been given as to how the data fit with how humans colonized the world. Here, I show that Neanderthal and Denisovan legacies are strongly correlated and that inferred legacy size, like heterozygosity, exhibits a strong correlation with distance from Africa. Simulations confirm that, once created, legacy size is extremely stable: it may reduce through admixture with lower legacy populations but cannot increase significantly through neutral drift. Consequently, populations carrying the highest legacies are likely to be those whose ancestors inter-bred most with archaics. However, the populations with the highest legacies are globally scattered and are unified, not by having origins within the known Neanderthal range, but instead by living in locations that lie furthest from Africa. Furthermore, the Simons Genome Diversity Project data reveal two distinct correlations between Neanderthal and Denisovan legacies, one that starts in North Africa and increases west to east across Eurasia and into some parts of Oceania, and a second, much steeper trend that starts in Africa, peaking with the San and Ju/'hoansi and which, if extrapolated, predicts the large inferred legacies of both archaics found in Oceania/Australia. Similar 'double' trends are observed for the introgression statistic f 4 in a second large dataset published by Qin and Stoneking (Qin &amp; Stoneking 2015 Mol. Biol. Evol. 32, 2665-2674 (doi:10.1093/molbev/msv141)). These trends appear at odds with simple models of how introgression occurred though more complicated patterns of introgression could potentially generate better fits. Moreover, substituting archaic genomes with those of great apes yields similar but biologically impossible signals of introgression, suggesting that the signals these metrics capture arise within humans and are largely independent of the test group. Interestingly, the data do appear to fit a speculative model in which the loss of diversity that occurred when humans moved further from Africa created a gradient in heterozygosity that in turn progressively reduced mutation rate such that populations furthest from Africa have diverged less from our common ancestor and hence from the archaics. In this light, the two distinct trends could be interpreted in terms of two 'out of Africa' events, an early one ending in Oceania and Australia and a later one that colonized Eurasia and the Americas.}, }
@article {pmid34148308, year = {2021}, author = {Jeworutzki, E and Tüttelmann, F and Rothenberg, I and Pusch, M and Schreiber, JA and Kliesch, S and Wünsch, B and Strutz-Seebohm, N and Seebohm, G}, title = {Can Unlikely Neanderthal Chloride Channel CLC-2 Gene Variants Provide Insights in Modern Human Infertility?.}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology}, volume = {55}, number = {3}, pages = {301-310}, doi = {10.33594/000000376}, pmid = {34148308}, issn = {1421-9778}, support = {CRU326//Deutsche Forschungsgemeinschaft (DFG)/Germany ; GRK2515//Deutsche Forschungsgemeinschaft (DFG)/Germany ; #IG21558//Fondazione AIRC per la Ricerca sul Cancro/Italy ; PRIN 20174TB8KW//Italian Research Ministry/Italy ; }, mesh = {Animals ; CLC-2 Chloride Channels ; *Chloride Channels/genetics/metabolism ; *Genetic Variation ; Humans ; *Infertility, Male ; Male ; *Neanderthals/genetics/metabolism ; Oocytes/metabolism ; Xenopus laevis ; }, abstract = {BACKGROUND/AIMS: Neanderthals, although well adapted to local environments, were rapidly replaced by anatomically modern humans (AMH) for unknown reasons. Genetic information on Neanderthals is limited restricting applicability of standard population genetics.<br><br>METHODS: Here, we apply a novel combination of restricted genetic analyses on preselected physiological key players (ion channels), electrophysiological analyses of gene variants of unclear significance expressed in Xenopus laevis oocytes using two electrode voltage clamp and transfer of results to AMH genetics. Using genetic screening in infertile men identified a loss of CLC-2 associated with sperm deficiency.<br><br>RESULTS: Increased genetic variation caused functionally impaired Neanderthals CLC-2 channels.<br><br>CONCLUSION: Increased genetic variation could reflect an adaptation to different local salt supplies at the cost of reduced sperm density. Interestingly and consistent with this hypothesis, lack of CLC-2 protein in a patient associates with high blood K[+] concentration and azoospermia.}, }
@article {pmid34140364, year = {2021}, author = {Gibbons, A}, title = {Genomes offer rare glimpse of Neanderthal family groups.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6548}, pages = {1251-1252}, doi = {10.1126/science.372.6548.1251}, pmid = {34140364}, issn = {1095-9203}, mesh = {Animals ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Family ; Female ; *Genome ; Male ; Neanderthals/*genetics ; Sociological Factors ; Y Chromosome ; }, }
@article {pmid34132815, year = {2021}, author = {Levi, G and de Lombares, C and Giuliani, C and Iannuzzi, V and Aouci, R and Garagnani, P and Franceschi, C and Grimaud-Hervé, D and Narboux-Nême, N}, title = {DLX5/6 GABAergic Expression Affects Social Vocalization: Implications for Human Evolution.}, journal = {Molecular biology and evolution}, volume = {38}, number = {11}, pages = {4748-4764}, pmid = {34132815}, issn = {1537-1719}, mesh = {Animals ; Genes, Homeobox ; Homeodomain Proteins/genetics/metabolism ; Humans ; Mice ; *Neanderthals/genetics ; Transcription Factors/genetics/metabolism ; *Transcription Factors, TFII/genetics ; Vocalization, Animal ; }, abstract = {DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated with neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioral and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10 min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1,400 calls/10 min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull, and brain shape…) overlap those affected in the "domestication syndrome". We therefore explored the possibility that DLX5/6 played a role in human evolution and "self-domestication" comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identified an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated with Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105 years of age), a well-established human model of healthy aging and longevity, suggesting their involvement in the coevolution of longevity, sociability, and speech.}, }
@article {pmid34117635, year = {2021}, author = {Antonio, P and Costantino, B and Silvia, C and Marina, M and Paolo, P and Alessio, V and Pasquale, R}, title = {Arothron: An R package for geometric morphometric methods and virtual anthropology applications.}, journal = {American journal of physical anthropology}, volume = {176}, number = {1}, pages = {144-151}, doi = {10.1002/ajpa.24340}, pmid = {34117635}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Anthropometry/*methods ; Bone and Bones/*anatomy &amp; histology/diagnostic imaging ; Female ; Fossils/*anatomy &amp; histology/diagnostic imaging ; Humans ; Imaging, Three-Dimensional/*methods ; Male ; Neanderthals ; *Software ; Tooth/anatomy &amp; histology/diagnostic imaging ; }, abstract = {OBJECTIVES: The statistical analysis of fossil remains is essential to understand the evolution of the genus Homo. Unfortunately, the human fossil record is straight away scarce and plagued with severe loss of information caused by taphonomic processes. The recently developed field of Virtual Anthropology helps to ameliorate this situation by using digital techniques to restore damaged and incomplete fossils.<br><br>MATERIALS AND METHODS: We present the package Arothron, an R software suite meant to process and analyze digital models of skeletal elements. Arothron includes tools to digitally extract virtual cavities such as cranial endocasts, to statistically align disarticulated or broken bony elements, and to visualize local variations between surface meshes and landmark configurations.<br><br>RESULTS: We describe the main functionalities of Arothron and illustrate their usage through reproducible case studies. We describe a tool for segmentation of skeletal cavities by showing its application on a malleus bone, a Neanderthal tooth, and a modern human cranium, reproducing their shape and calculating their volume. We illustrate how to digitally align a disarticulated model of a modern human cranium, and how to combine piecemeal shape information on individual specimens into one. In addition, we present useful visualization tools by comparing the morphological differences between the right hemisphere of the Neanderthal and the modern human brain.<br><br>CONCLUSIONS: The Arothron R package is designed to study digital models of fossil specimens. By using Arothron, scientists can handle digital models with ease, investigate the inner morphology of 3D skeletal models, gain a full representation of the original shapes of damaged specimens, and compare shapes across specimens.}, }
@article {pmid34117310, year = {2021}, author = {Singh, PP and Srivastava, A and Sultana, GNN and Khanam, N and Pathak, A and Suravajhala, P and Singh, R and Shrivastava, P and van Driem, G and Thangaraj, K and Chaubey, G}, title = {The major genetic risk factor for severe COVID-19 does not show any association among South Asian populations.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {12346}, pmid = {34117310}, issn = {2045-2322}, mesh = {Angiotensin-Converting Enzyme 2/genetics ; Asians/*genetics ; COVID-19/*pathology/virology ; Gene Frequency ; Genetic Loci ; Haplotypes ; Humans ; Polymorphism, Single Nucleotide ; Risk Factors ; SARS-CoV-2/isolation &amp; purification ; }, abstract = {With the growing evidence on the variable human susceptibility against COVID-19, it is evident that some genetic loci modulate the severity of the infection. Recent studies have identified several loci associated with greater severity. More recently, a study has identified a 50 kb genomic segment introgressed from Neanderthal adding a risk for COVID-19, and this genomic segment is present among 16% and 50% people of European and South Asian descent, respectively. Our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations, respectively, which appears to be responsible for the low case fatality rate among South Asian populations. This result was also consistent with the real-time infection rate and case fatality rate among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the real-time infection rates and case fatality rate in India. We found that the polymorphism present in the 50 kb introgressed genomic segment (rs10490770) did not show any significant correlation with the infection and case fatality rate in India.}, }
@article {pmid34095864, year = {2021}, author = {Zhou, Y and Browning, SR}, title = {Protocol for detecting introgressed archaic variants with SPrime.}, journal = {STAR protocols}, volume = {2}, number = {2}, pages = {100550}, pmid = {34095864}, issn = {2666-1667}, support = {R01 HG010869/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient/analysis ; Genetic Introgression/*genetics ; Genomics/*methods ; Hominidae/genetics ; Humans ; Neanderthals/*genetics ; }, abstract = {The SPrime program detects the variants in current-day populations that were introgressed from an archaic source in the past. It is optimized for detecting introgression from Neanderthals and Denisovans in modern humans. We provide a protocol for detecting Neanderthal and Denisovan introgression in 1000 Genomes Project data, specifically focusing on the CHB (Han Chinese in Beijing) population. For complete details on the use and execution of this protocol, please refer to Browning et al. (2018).}, }
@article {pmid34079134, year = {2021}, author = {Barras, C}, title = {How did Neanderthals and other ancient humans learn to count?.}, journal = {Nature}, volume = {594}, number = {7861}, pages = {22-25}, pmid = {34079134}, issn = {1476-4687}, mesh = {Animals ; *Archaeology ; *Bone and Bones ; Cognition ; Cultural Evolution/*history ; History, Ancient ; Humans ; Inventions/history ; Mathematics/*history ; Neanderthals/*psychology ; Pan troglodytes/psychology ; Selection, Genetic ; }, }
@article {pmid34073168, year = {2021}, author = {Folgerø, PO and Johansson, C and Stokkedal, LH}, title = {The Superior Visual Perception Hypothesis: Neuroaesthetics of Cave Art.}, journal = {Behavioral sciences (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, pmid = {34073168}, issn = {2076-328X}, abstract = {Cave Art in the Upper Paleolithic presents a boost of creativity and visual thinking. What can explain these savant-like paintings? The normal brain function in modern man rarely supports the creation of highly detailed paintings, particularly the convincing representation of animal movement, without extensive training and access to modern technology. Differences in neuro-signaling and brain anatomy between modern and archaic Homo sapiens could also cause differences in perception. The brain of archaic Homo sapiens could perceive raw detailed information without using pre-established top-down concepts, as opposed to the common understanding of the normal modern non-savant brain driven by top-down control. Some ancient genes preserved in modern humans may be expressed in rare disorders. Researchers have compared Cave Art with art made by people with autism spectrum disorder. We propose that archaic primary consciousness, as opposed to modern secondary consciousness, included a savant-like perception with a superior richness of details compared to modern man. Modern people with high frequencies of Neanderthal genes, have notable anatomical features such as increased skull width in the occipital and parietal visual areas. We hypothesize that the anatomical differences are functional and may allow a different path to visual perception.}, }
@article {pmid34066804, year = {2021}, author = {Yamamoto, N and Yamamoto, R and Ariumi, Y and Mizokami, M and Shimotohno, K and Yoshikura, H}, title = {Does Genetic Predisposition Contribute to the Exacerbation of COVID-19 Symptoms in Individuals with Comorbidities and Explain the Huge Mortality Disparity between the East and the West?.}, journal = {International journal of molecular sciences}, volume = {22}, number = {9}, pages = {}, pmid = {34066804}, issn = {1422-0067}, mesh = {Aged ; Alleles ; Angiotensin-Converting Enzyme 2/genetics/metabolism ; Animals ; COVID-19/*genetics/metabolism/physiopathology/virology ; Comorbidity ; *Genetic Predisposition to Disease ; HLA Antigens/genetics/metabolism ; Haplotypes ; Humans ; Inflammation/genetics/metabolism ; Neanderthals/genetics ; Peptidyl-Dipeptidase A/*genetics/metabolism ; Polymorphism, Genetic ; Risk Factors ; Severity of Illness Index ; }, abstract = {The elderly and patients with several comorbidities experience more severe cases of coronavirus disease 2019 (COVID-19) than healthy patients without underlying medical conditions. However, it is unclear why these people are prone to developing alveolar pneumonia, rapid exacerbations, and death. Therefore, we hypothesized that people with comorbidities may have a genetic predisposition that makes them more vulnerable to various factors; for example, they are likely to become more severely ill when infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To test this hypothesis, we searched the literature extensively. Polymorphisms of genes, such as those that encode angiotensin-converting enzyme 1 (ACE1), have been associated with numerous comorbidities, such as cardiovascular disease, hypertension, diabetes, chronic kidney disease, and obesity, and there are potential mechanisms to explain these associations (e.g., DD-type carriers have greater ACE1 activity, and patients with a genetic alpha-1 anti-trypsin (AAT) deficiency lack control over inflammatory mediators). Since comorbidities are associated with chronic inflammation and are closely related to the renin-angiotensin-aldosterone system (RAAS), these individuals may already have a mild ACE1/ACE2 imbalance before viral infection, which increases their risk for developing severe cases of COVID-19. However, there is still much debate about the association between ACE1 D/I polymorphism and comorbidities. The best explanation for this discrepancy could be that the D allele and DD subtypes are associated with comorbidities, but the DD genotype alone does not have an exceptionally large effect. This is also expected since the ACE1 D/I polymorphism is only an intron marker. We also discuss how polymorphisms of AAT and other genes are involved in comorbidities and the severity of SARS-CoV-2 infection. Presumably, a combination of multiple genes and non-genetic factors is involved in the establishment of comorbidities and aggravation of COVID-19.}, }
@article {pmid34051612, year = {2021}, author = {Salazar-García, DC and Power, RC and Rudaya, N and Kolobova, K and Markin, S and Krivoshapkin, A and Henry, AG and Richards, MP and Viola, B}, title = {Dietary evidence from Central Asian Neanderthals: A combined isotope and plant microremains approach at Chagyrskaya Cave (Altai, Russia).}, journal = {Journal of human evolution}, volume = {156}, number = {}, pages = {102985}, doi = {10.1016/j.jhevol.2021.102985}, pmid = {34051612}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; *Caves ; Diet/*history ; History, Ancient ; Humans ; Isotopes/analysis ; *Neanderthals ; *Plants ; Russia ; }, abstract = {Neanderthals are known primarily from their habitation of Western Eurasia, but they also populated large expanses of Northern Asia for thousands of years. Owing to a sparse archaeological record, relatively little is known about these eastern Neanderthal populations. Unlike in their western range, there are limited zooarchaeological and paleobotanical studies that inform us about the nature of their subsistence. Here, we perform a combined analysis of carbon and nitrogen stable isotopes on bone collagen and microbotanical remains in dental calculus to reconstruct the diet of eastern Neanderthals at Chagyrskaya Cave in the Altai Mountains of Southern Siberia, Russia. Stable isotopes identify one individual as possessing a high trophic level due to the hunting of large- and medium-sized ungulates, while the analysis of dental calculus also indicates the presence of plants in the diet of this individual and others from the site. These findings indicate eastern Neanderthals may have had broadly similar subsistence patterns to those elsewhere in their range.}, }
@article {pmid34034800, year = {2021}, author = {Quan, C and Li, Y and Liu, X and Wang, Y and Ping, J and Lu, Y and Zhou, G}, title = {Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {159}, pmid = {34034800}, issn = {1474-760X}, mesh = {Adaptation, Physiological/*genetics ; *Altitude ; Animals ; Ethnicity/genetics ; *Genomic Structural Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Neanderthals/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Tibet ; Young Adult ; }, abstract = {BACKGROUND: Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. However, few studies have examined the role of SVs in high-altitude adaptation and little is known of adaptive introgressed SVs in Tibetans so far.<br><br>RESULTS: Here, we generate a comprehensive catalog of SVs in a Chinese Tibetan (n = 15) and Han (n = 10) population using nanopore sequencing technology. Among a total of 38,216 unique SVs in the catalog, 27% are sequence-resolved for the first time. We systematically assess the distribution of these SVs across repeat sequences and functional genomic regions. Through genotyping in additional 276 genomes, we identify 69 Tibetan-Han stratified SVs and 80 candidate adaptive genes. We also discover a few adaptive introgressed SV candidates and provide evidence for a deletion of 335 base pairs at 1p36.32.<br><br>CONCLUSIONS: Overall, our results highlight the important role of SVs in the evolutionary processes of Tibetans' adaptation to the Qinghai-Tibet Plateau and provide a valuable resource for future high-altitude adaptation studies.}, }
@article {pmid34031254, year = {2021}, author = {Higham, TFG and Douka, K}, title = {The reliability of late radiocarbon dates from the Paleolithic of southern China.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {22}, pages = {}, pmid = {34031254}, issn = {1091-6490}, mesh = {Animals ; China ; *Neanderthals ; *Radiometric Dating ; Reproducibility of Results ; }, }
@article {pmid34028527, year = {2021}, author = {Ahlquist, KD and Bañuelos, MM and Funk, A and Lai, J and Rong, S and Villanea, FA and Witt, KE}, title = {Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture.}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {34028527}, issn = {1759-6653}, support = {T32 GM007601/GM/NIGMS NIH HHS/United States ; R35 GM139628/GM/NIGMS NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; R01 GM127472/GM/NIGMS NIH HHS/United States ; R01 GM118652/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Genome, Human ; Genomics ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Pedigree ; }, abstract = {The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.}, }
@article {pmid34020296, year = {2021}, author = {Spindler, L and Comeskey, D and Chabai, V and Uthmeier, T and Buckley, M and Devièse, T and Higham, T}, title = {Dating the last Middle Palaeolithic of the Crimean Peninsula: New hydroxyproline AMS dates from the site of Kabazi II.}, journal = {Journal of human evolution}, volume = {156}, number = {}, pages = {102996}, doi = {10.1016/j.jhevol.2021.102996}, pmid = {34020296}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; *Fossils ; History, Ancient ; Hydroxyproline/*analysis ; Neanderthals ; Radiometric Dating ; }, abstract = {Radiocarbon dating of bone and charcoal from sites dating to the Middle and Upper Paleolithic is challenging due to low residual levels of radiocarbon. This means that small amounts of contaminating carbon can wield a great influence over accuracy unless they are fully removed. The site of Kabazi II in the Crimea is important because radiocarbon dates previously obtained from bones in archaeological horizons that date to the Western Crimean Mousterian (WCM) are surprisingly young. We redated the same samples using a single compound dating method that focuses on extracting and dating the amino acid hydroxyproline. We show that single amino acid dates produce significantly older determinations than those that use bulk collagen pretreatment procedures. Our results suggest that instead of dating to 35,000-40,000 cal BP, the bones actually date to >50,000 cal BP. This implies that the WCM at this site is much older than previously thought. In light of these current findings, we considered the dates of other key Crimean sites and concluded that in the absence of reliable pretreatment methods, it would be wise to consider many of them minimum ages. We conclude that there is little robust evidence to suggest Neanderthals were present in the Crimea after 40,000 cal BP.}, }
@article {pmid34010592, year = {2021}, author = {Svensson, E and Günther, T and Hoischen, A and Hervella, M and Munters, AR and Ioana, M and Ridiche, F and Edlund, H and van Deuren, RC and Soficaru, A and de-la-Rua, C and Netea, MG and Jakobsson, M}, title = {Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.}, journal = {Current biology : CB}, volume = {31}, number = {14}, pages = {2973-2983.e9}, doi = {10.1016/j.cub.2021.04.045}, pmid = {34010592}, issn = {1879-0445}, mesh = {Animals ; Emigration and Immigration ; Europe ; Female ; Genome, Human ; Humans ; Infant, Newborn ; *Neanderthals/genetics ; Skull ; }, abstract = {Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Peştera Muierii," Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.}, }
@article {pmid33992907, year = {2021}, author = {Kerner, G and Patin, E and Quintana-Murci, L}, title = {New insights into human immunity from ancient genomics.}, journal = {Current opinion in immunology}, volume = {72}, number = {}, pages = {116-125}, pmid = {33992907}, issn = {1879-0372}, mesh = {Animals ; COVID-19/epidemiology/genetics/*immunology ; Evolution, Molecular ; Genetic Predisposition to Disease ; Genetics, Population ; Genomics ; Hominidae ; Humans ; Immunity/*genetics ; SARS-CoV-2/*physiology ; }, abstract = {Population genetic studies have clearly indicated that immunity and host defense are among the functions most frequently subject to natural selection, and increased our understanding of the biological relevance of the corresponding genes and their contribution to variable immune traits and diseases. Herein, we will focus on some recently studied forms of human adaptation to infectious agents, including hybridization with now-extinct hominins, such as Neanderthals and Denisovans, and admixture between modern human populations. These studies, which are partly enabled by the technological advances in the sequencing of DNA from ancient remains, provide new insight into the sources of immune response variation in contemporary humans, such as the recently reported link between Neanderthal heritage and susceptibility to severe COVID-19 disease. Furthermore, ancient DNA analyses, in both humans and pathogens, allow to measure the action of natural selection on immune genes across time and to reconstruct the impact of past epidemics on the evolution of human immunity.}, }
@article {pmid33974862, year = {2021}, author = {Harvati, K}, title = {Katerina Harvati.}, journal = {Current biology : CB}, volume = {31}, number = {9}, pages = {R418-R419}, doi = {10.1016/j.cub.2021.04.003}, pmid = {33974862}, issn = {1879-0445}, mesh = {Animals ; Biological Evolution ; Fossils ; History, 20th Century ; History, 21st Century ; Humans ; Interdisciplinary Communication ; Mentors ; *Neanderthals ; *Paleontology/education ; }, abstract = {Interview with paleoanthropologist Katerina Harvati, who studies Neanderthal evolution and modern human origins at the Eberhard Karls University of Tübingen.}, }
@article {pmid33972424, year = {2021}, author = {Fellows Yates, JA and Velsko, IM and Aron, F and Posth, C and Hofman, CA and Austin, RM and Parker, CE and Mann, AE and Nägele, K and Arthur, KW and Arthur, JW and Bauer, CC and Crevecoeur, I and Cupillard, C and Curtis, MC and Dalén, L and Díaz-Zorita Bonilla, M and Díez Fernández-Lomana, JC and Drucker, DG and Escribano Escrivá, E and Francken, M and Gibbon, VE and González Morales, MR and Grande Mateu, A and Harvati, K and Henry, AG and Humphrey, L and Menéndez, M and Mihailović, D and Peresani, M and Rodríguez Moroder, S and Roksandic, M and Rougier, H and Sázelová, S and Stock, JT and Straus, LG and Svoboda, J and Teßmann, B and Walker, MJ and Power, RC and Lewis, CM and Sankaranarayanan, K and Guschanski, K and Wrangham, RW and Dewhirst, FE and Salazar-García, DC and Krause, J and Herbig, A and Warinner, C}, title = {The evolution and changing ecology of the African hominid oral microbiome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {20}, pages = {}, pmid = {33972424}, issn = {1091-6490}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 GM089886/GM/NIGMS NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Africa ; Animals ; Bacteria/classification/genetics ; Biofilms ; *Biological Evolution ; Dental Plaque/microbiology ; Ecology/*methods ; Geography ; Gorilla gorilla/microbiology ; Hominidae/classification/*microbiology ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; Mouth/*microbiology ; Pan troglodytes/microbiology ; Phylogeny ; }, abstract = {The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.}, }
@article {pmid33951239, year = {2021}, author = {Gopalan, S and Atkinson, EG and Buck, LT and Weaver, TD and Henn, BM}, title = {Inferring archaic introgression from hominin genetic data.}, journal = {Evolutionary anthropology}, volume = {30}, number = {3}, pages = {199-220}, pmid = {33951239}, issn = {1520-6505}, support = {R35 GM133531/GM/NIGMS NIH HHS/United States ; K12-GM102778/NH/NIH HHS/United States ; K01-MH121659/NH/NIH HHS/United States ; R35-GM133531/NH/NIH HHS/United States ; K01 MH121659/MH/NIMH NIH HHS/United States ; K12 GM102778/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Genetic Introgression/*genetics ; Hominidae/classification/genetics ; Humans ; Neanderthals/classification/*genetics ; }, abstract = {Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.}, }
@article {pmid33942714, year = {2021}, author = {Stepanova, V and Moczulska, KE and Vacano, GN and Kurochkin, I and Ju, X and Riesenberg, S and Macak, D and Maricic, T and Dombrowski, L and Schörnig, M and Anastassiadis, K and Baker, O and Naumann, R and Khrameeva, E and Vanushkina, A and Stekolshchikova, E and Egorova, A and Tkachev, A and Mazzarino, R and Duval, N and Zubkov, D and Giavalisco, P and Wilkinson, TG and Patterson, D and Khaitovich, P and Pääbo, S}, title = {Reduced purine biosynthesis in humans after their divergence from Neandertals.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33942714}, issn = {2050-084X}, mesh = {Animals ; Biosynthetic Pathways/*genetics ; Female ; Gene Editing ; Humans ; Macaca/metabolism ; Male ; Metabolome/*genetics ; Mice ; Mice, Transgenic ; Mutation, Missense ; Neanderthals/*metabolism ; Pan troglodytes/metabolism ; Purines/*biosynthesis/*metabolism ; }, abstract = {We analyze the metabolomes of humans, chimpanzees, and macaques in muscle, kidney and three different regions of the brain. Although several compounds in amino acid metabolism occur at either higher or lower concentrations in humans than in the other primates, metabolites downstream of adenylosuccinate lyase, which catalyzes two reactions in purine synthesis, occur at lower concentrations in humans. This enzyme carries an amino acid substitution that is present in all humans today but absent in Neandertals. By introducing the modern human substitution into the genomes of mice, as well as the ancestral, Neandertal-like substitution into the genomes of human cells, we show that this amino acid substitution contributes to much or all of the reduction of de novo synthesis of purines in humans.}, }
@article {pmid33934123, year = {2021}, author = {Mualim, K and Theunert, C and Slatkin, M}, title = {Estimation of coalescence probabilities and population divergence times from SNP data.}, journal = {Heredity}, volume = {127}, number = {1}, pages = {1-9}, pmid = {33934123}, issn = {1365-2540}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Humans ; *Neanderthals/genetics ; Population Density ; Probability ; }, abstract = {We present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al. (2014) to test whether an archaic genome is from a population directly ancestral to a present-day population. The G(A|B) method does not require distinguishing ancestral from derived alleles or assumptions about demographic history before population divergence. We discuss the relationship of our method to two similar methods, one introduced by Green et al. (2010) and called the F(A|B) method and the other introduced by Schlebusch et al. (2017) and called the TT method. When our method is applied to individuals from three or more populations, it provides a test of whether the population history is treelike because coalescence probabilities are additive on a tree. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.}, }
@article {pmid33892510, year = {2021}, author = {Villanea, FA and Huerta-Sanchez, E and Fox, K}, title = {ABO Genetic Variation in Neanderthals and Denisovans.}, journal = {Molecular biology and evolution}, volume = {38}, number = {8}, pages = {3373-3382}, pmid = {33892510}, issn = {1537-1719}, support = {R35 GM128946/GM/NIGMS NIH HHS/United States ; }, mesh = {ABO Blood-Group System/*genetics ; Animals ; Genetic Variation ; Genome, Human ; Haplotypes ; Humans ; Neanderthals/*genetics ; }, abstract = {Variation at the ABO locus was one of the earliest sources of data in the study of human population identity and history, and to this day remains widely genotyped due to its importance in blood and tissue transfusions. Here, we look at ABO blood type variants in our archaic relatives: Neanderthals and Denisovans. Our goal is to understand the genetic landscape of the ABO gene in archaic humans, and how it relates to modern human ABO variation. We found two Neanderthal variants of the O allele in the Siberian Neanderthals (O1 and O2), one of these variants is shared with an European Neanderthal, who is a heterozygote for this O1 variant and a rare cis-AB variant. The Denisovan individual is heterozygous for two variants of the O1 allele, functionally similar to variants found widely in modern humans. Perhaps more surprisingly, the O2 allele variant found in Siberian Neanderthals can be found at low frequencies in modern Europeans and Southeast Asians, and the O1 allele variant found in Siberian and European Neanderthal is also found at very low frequency in modern East Asians. Our genetic distance analyses suggest both alleles survive in modern humans due to inbreeding with Neanderthals. We find that the sequence backgrounds of the surviving Neanderthal-like O alleles in modern humans retain a higher sequence divergence than other surviving Neanderthal genome fragments, supporting a view of balancing selection operating in the Neanderthal ABO alleles by retaining highly diverse haplotypes compared with portions of the genome evolving neutrally.}, }
@article {pmid33885362, year = {2021}, author = {Weiss, CV and Harshman, L and Inoue, F and Fraser, HB and Petrov, DA and Ahituv, N and Gokhman, D}, title = {The cis-regulatory effects of modern human-specific variants.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33885362}, issn = {2050-084X}, support = {U01 MH116438/MH/NIMH NIH HHS/United States ; 1U01MH116438/MH/NIMH NIH HHS/United States ; UM1 HG009408/HG/NHGRI NIH HHS/United States ; P01 HD084387/HD/NICHD NIH HHS/United States ; 1R01MH109907/MH/NIMH NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; 1UM1HG009408/HG/NHGRI NIH HHS/United States ; F31 HG011568/HG/NHGRI NIH HHS/United States ; }, mesh = {Embryonic Stem Cells/*metabolism ; *Gene Expression Regulation ; Genome, Human ; Humans ; Osteoblasts/*metabolism ; *Polymorphism, Single Nucleotide ; Stem Cells/*metabolism ; Transcription Factors/*metabolism ; }, abstract = {The Neanderthal and Denisovan genomes enabled the discovery of sequences that differ between modern and archaic humans, the majority of which are noncoding. However, our understanding of the regulatory consequences of these differences remains limited, in part due to the decay of regulatory marks in ancient samples. Here, we used a massively parallel reporter assay in embryonic stem cells, neural progenitor cells, and bone osteoblasts to investigate the regulatory effects of the 14,042 single-nucleotide modern human-specific variants. Overall, 1791 (13%) of sequences containing these variants showed active regulatory activity, and 407 (23%) of these drove differential expression between human groups. Differentially active sequences were associated with divergent transcription factor binding motifs, and with genes enriched for vocal tract and brain anatomy and function. This work provides insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.}, }
@article {pmid33882583, year = {2022}, author = {Spiegelhalder, P and Bögemann, M}, title = {[Non-metastatic castration-resistant prostate cancer (M0CRPC) - Apalutamide in high-risk M0CRPC: case reports from the SPARTAN study and the apalutamide compassionate use program].}, journal = {Aktuelle Urologie}, volume = {53}, number = {1}, pages = {60-63}, doi = {10.1055/a-1338-0202}, pmid = {33882583}, issn = {1438-8820}, mesh = {Androgen Antagonists/therapeutic use ; *Compassionate Use Trials ; Humans ; Male ; *Prostatic Neoplasms, Castration-Resistant/drug therapy ; Thiohydantoins/therapeutic use ; }, abstract = {The occurrence of distant metastases represents a prognostically unfavourable turning point in non-metastatic castration-resistant prostate cancer (M0CRPC). M0CRPC patients with a short PSA doubling time have a particularly high risk of progression. For a long time, there was no further treatment option for these patients apart from watchful waiting while maintaining classic androgen deprivation therapy (ADT). Apalutamide, a next-generation anti-androgen available since January 2019, significantly increased metastasis-free survival compared with placebo in the pivotal SPARTAN trial in patients with high-risk M0CRPC. The presented patient cases from SPARTAN and the apalutamide compassionate use program are examples of the beneficial effects that apalutamide can achieve in the M0CRPC setting.}, }
@article {pmid33879864, year = {2022}, author = {Zwir, I and Del-Val, C and Hintsanen, M and Cloninger, KM and Romero-Zaliz, R and Mesa, A and Arnedo, J and Salas, R and Poblete, GF and Raitoharju, E and Raitakari, O and Keltikangas-Järvinen, L and de Erausquin, GA and Tattersall, I and Lehtimäki, T and Cloninger, CR}, title = {Evolution of genetic networks for human creativity.}, journal = {Molecular psychiatry}, volume = {27}, number = {1}, pages = {354-376}, pmid = {33879864}, issn = {1476-5578}, mesh = {Animals ; Brain ; *Creativity ; Evolution, Molecular ; *Gene Regulatory Networks ; Humans ; Neanderthals/genetics ; Pan troglodytes/genetics ; *RNA, Long Noncoding/genetics ; }, abstract = {The genetic basis for the emergence of creativity in modern humans remains a mystery despite sequencing the genomes of chimpanzees and Neanderthals, our closest hominid relatives. Data-driven methods allowed us to uncover networks of genes distinguishing the three major systems of modern human personality and adaptability: emotional reactivity, self-control, and self-awareness. Now we have identified which of these genes are present in chimpanzees and Neanderthals. We replicated our findings in separate analyses of three high-coverage genomes of Neanderthals. We found that Neanderthals had nearly the same genes for emotional reactivity as chimpanzees, and they were intermediate between modern humans and chimpanzees in their numbers of genes for both self-control and self-awareness. 95% of the 267 genes we found only in modern humans were not protein-coding, including many long-non-coding RNAs in the self-awareness network. These genes may have arisen by positive selection for the characteristics of human well-being and behavioral modernity, including creativity, prosocial behavior, and healthy longevity. The genes that cluster in association with those found only in modern humans are over-expressed in brain regions involved in human self-awareness and creativity, including late-myelinating and phylogenetically recent regions of neocortex for autobiographical memory in frontal, parietal, and temporal regions, as well as related components of cortico-thalamo-ponto-cerebellar-cortical and cortico-striato-cortical loops. We conclude that modern humans have more than 200 unique non-protein-coding genes regulating co-expression of many more protein-coding genes in coordinated networks that underlie their capacities for self-awareness, creativity, prosocial behavior, and healthy longevity, which are not found in chimpanzees or Neanderthals.}, }
@article {pmid33860534, year = {2021}, author = {Yi, Z and Zanolli, C and Liao, W and Wang, W}, title = {A deep-learning-based workflow to assess taxonomic affinity of hominid teeth with a test on discriminating Pongo and Homo upper molars.}, journal = {American journal of physical anthropology}, volume = {175}, number = {4}, pages = {931-942}, doi = {10.1002/ajpa.24286}, pmid = {33860534}, issn = {1096-8644}, mesh = {Animals ; *Deep Learning ; Dentin ; *Hominidae ; Humans ; Pongo ; Workflow ; }, abstract = {OBJECTIVES: Convolutional neural network (CNN) is a state-of-art deep learning (DL) method with superior performance in image classification. Here, a CNN-based workflow is proposed to discriminate hominid teeth. Our hope is that this method could help confirm otherwise questionable records of Homo from Pleistocene deposits where there is a standing risk of mis-attributing molars of Pongo to Homo.<br><br>METHODS AND MATERIALS: A two-step workflow was designed. The first step is converting the enamel-dentine junction (EDJ) into EDJ card, that is, a two-dimensional image conversion of the three-dimensional EDJ surface. In this step, researchers must carefully orient the teeth according to the cervical plane. The second step is training the CNN learner with labeled EDJ cards. A sample consisting of 53 fossil Pongo and 53 Homo (modern human and Neanderthal) was adopted to generate EDJ cards, which were then separated into training set (n&#xa0;=&#x2009;84) and validation set (n&#xa0;=&#x2009;22). To assess the feasibility of this workflow, a Pongo-Homo classifier was trained from the aforementioned EDJ card set, and then the classifier was used to predict the taxonomic affinities of six samples (test set) from von Koenigswald's Chinese Apothecary collection.<br><br>RESULTS: Results show that EDJ cards in validation set are classified accurately by the CNN learner. More importantly, taxonomic predictions for six specimens in test set match well with the diagnosis results deduced from multiple lines of evidence, implying the great potential of CNN method.<br><br>DISCUSSION: This workflow paves a way for future studies using CNN to address taxonomic complexity (e.g., distinguishing Pongo and Homo teeth from the Pleistocene of Asia). Further improvements include visual interpretation and extending the applicability to moderately worn teeth.}, }
@article {pmid33859012, year = {2021}, author = {Gibbons, A}, title = {DNA from cave dirt traces Neanderthal upheaval.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6539}, pages = {222-223}, doi = {10.1126/science.372.6539.222}, pmid = {33859012}, issn = {1095-9203}, mesh = {Animals ; Caves ; DNA ; *Hominidae/genetics ; *Neanderthals/genetics ; }, }
@article {pmid33858989, year = {2021}, author = {Vernot, B and Zavala, EI and Gómez-Olivencia, A and Jacobs, Z and Slon, V and Mafessoni, F and Romagné, F and Pearson, A and Petr, M and Sala, N and Pablos, A and Aranburu, A and de Castro, JMB and Carbonell, E and Li, B and Krajcarz, MT and Krivoshapkin, AI and Kolobova, KA and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Viola, B and Grote, S and Essel, E and Herráez, DL and Nagel, S and Nickel, B and Richter, J and Schmidt, A and Peter, B and Kelso, J and Roberts, RG and Arsuaga, JL and Meyer, M}, title = {Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6542}, pages = {}, doi = {10.1126/science.abf1667}, pmid = {33858989}, issn = {1095-9203}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Caves/chemistry ; Cell Nucleus/*genetics ; DNA, Mitochondrial/analysis/*genetics/isolation &amp; purification ; Geologic Sediments/chemistry ; Neanderthals/*classification/*genetics ; Phylogeny ; Population/genetics ; Sequence Analysis, DNA ; Siberia ; Spain ; }, abstract = {Bones and teeth are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites. Mitochondrial DNA (mtDNA) has been retrieved from cave sediments but provides limited value for studying population relationships. We therefore developed methods for the enrichment and analysis of nuclear DNA from sediments and applied them to cave deposits in western Europe and southern Siberia dated to between 200,000 and 50,000 years ago. We detected a population replacement in northern Spain about 100,000 years ago, which was accompanied by a turnover of mtDNA. We also identified two radiation events in Neanderthal history during the early part of the Late Pleistocene. Our work lays the ground for studying the population history of ancient hominins from trace amounts of nuclear DNA in sediments.}, }
@article {pmid33854233, year = {2021}, author = {Choin, J and Mendoza-Revilla, J and Arauna, LR and Cuadros-Espinoza, S and Cassar, O and Larena, M and Ko, AM and Harmant, C and Laurent, R and Verdu, P and Laval, G and Boland, A and Olaso, R and Deleuze, JF and Valentin, F and Ko, YC and Jakobsson, M and Gessain, A and Excoffier, L and Stoneking, M and Patin, E and Quintana-Murci, L}, title = {Genomic insights into population history and biological adaptation in Oceania.}, journal = {Nature}, volume = {592}, number = {7855}, pages = {583-589}, pmid = {33854233}, issn = {1476-4687}, mesh = {Adaptation, Biological/*genetics ; Animals ; Australia ; *Biological Evolution ; Datasets as Topic ; Far East ; Genetic Introgression ; *Genetics, Population ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/*history ; Humans ; *Islands ; Native Hawaiian or Other Pacific Islander/*genetics ; Neanderthals/genetics ; Oceania ; Pacific Ocean ; Taiwan ; }, abstract = {The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes[1]. However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related ('Near Oceanian') groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000-40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago[2-4]. Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.}, }
@article {pmid33850254, year = {2021}, author = {Vaesen, K and Dusseldorp, GL and Brandt, MJ}, title = {Author Correction: An emerging consensus in palaeoanthropology: demography was the main factor responsible for the disappearance of Neanderthals.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {8450}, doi = {10.1038/s41598-021-88189-5}, pmid = {33850254}, issn = {2045-2322}, }
@article {pmid33833103, year = {2021}, author = {Gibbons, A}, title = {When modern humans met Neanderthals.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6538}, pages = {115-116}, doi = {10.1126/science.372.6538.115}, pmid = {33833103}, issn = {1095-9203}, mesh = {Animals ; Bulgaria ; Czech Republic ; *DNA, Ancient ; Female ; Genetics, Population ; *Genome, Human ; Hominidae/*genetics ; Humans ; Male ; Neanderthals/*genetics ; Sexual Behavior ; Sexual Behavior, Animal ; }, }
@article {pmid33828320, year = {2021}, author = {Hajdinjak, M and Mafessoni, F and Skov, L and Vernot, B and Hübner, A and Fu, Q and Essel, E and Nagel, S and Nickel, B and Richter, J and Moldovan, OT and Constantin, S and Endarova, E and Zahariev, N and Spasov, R and Welker, F and Smith, GM and Sinet-Mathiot, V and Paskulin, L and Fewlass, H and Talamo, S and Rezek, Z and Sirakova, S and Sirakov, N and McPherron, SP and Tsanova, T and Hublin, JJ and Peter, BM and Meyer, M and Skoglund, P and Kelso, J and Pääbo, S}, title = {Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry.}, journal = {Nature}, volume = {592}, number = {7853}, pages = {253-257}, pmid = {33828320}, issn = {1476-4687}, support = {852558/ERC_/European Research Council/International ; FC001595/MRC_/Medical Research Council/United Kingdom ; FC001595//Wellcome Trust/United Kingdom ; 694707/ERC_/European Research Council/International ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Alleles ; Americas/ethnology ; Animals ; Archaeology ; Bulgaria/ethnology ; Caves ; DNA, Ancient/*analysis ; Far East/ethnology ; Female ; Genome, Human/*genetics ; History, Ancient ; Humans ; Male ; Neanderthals/*genetics ; Phylogeny ; }, abstract = {Modern humans appeared in Europe by at least 45,000 years ago[1-5], but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago[6], and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria[1,2]. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania[7] and Siberia[8] who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.}, }
@article {pmid33828282, year = {2021}, author = {Callaway, E}, title = {Oldest DNA from a Homo sapiens reveals surprisingly recent Neanderthal ancestry.}, journal = {Nature}, volume = {592}, number = {7854}, pages = {339}, pmid = {33828282}, issn = {1476-4687}, mesh = {Animals ; DNA/genetics ; Fossils ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; }, }
@article {pmid33828250, year = {2021}, author = {Lalueza-Fox, C}, title = {Neanderthal assimilation?.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {6}, pages = {711-712}, pmid = {33828250}, issn = {2397-334X}, mesh = {Animals ; Czech Republic ; Genome ; *Hominidae/genetics ; Humans ; Infant, Newborn ; *Neanderthals/genetics ; Skull ; }, }
@article {pmid33828249, year = {2021}, author = {Prüfer, K and Posth, C and Yu, H and Stoessel, A and Spyrou, MA and Deviese, T and Mattonai, M and Ribechini, E and Higham, T and Velemínský, P and Brůžek, J and Krause, J}, title = {A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {6}, pages = {820-825}, pmid = {33828249}, issn = {2397-334X}, mesh = {Africa ; Czech Republic ; Europe ; Female ; Humans ; Infant, Newborn ; Middle East ; Siberia ; *Skull ; }, abstract = {Modern humans expanded into Eurasia more than 40,000 years ago following their dispersal out of Africa. These Eurasians carried ~2-3% Neanderthal ancestry in their genomes, originating from admixture with Neanderthals that took place sometime between 50,000 and 60,000 years ago, probably in the Middle East. In Europe, the modern human expansion preceded the disappearance of Neanderthals from the fossil record by 3,000-5,000 years. The genetic makeup of the first Europeans who colonized the continent more than 40,000 years ago remains poorly understood since few specimens have been studied. Here, we analyse a genome generated from the skull of a female individual from Zlatý kůň, Czechia. We found that she belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians. Her genome carries ~3% Neanderthal ancestry, similar to those of other Upper Palaeolithic hunter-gatherers. However, the lengths of the Neanderthal segments are longer than those observed in the currently oldest modern human genome of the ~45,000-year-old Ust'-Ishim individual from Siberia, suggesting that this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa.}, }
@article {pmid33798098, year = {2021}, author = {Devièse, T and Abrams, G and Hajdinjak, M and Pirson, S and De Groote, I and Di Modica, K and Toussaint, M and Fischer, V and Comeskey, D and Spindler, L and Meyer, M and Semal, P and Higham, T}, title = {Reevaluating the timing of Neanderthal disappearance in Northwest Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {12}, pages = {}, pmid = {33798098}, issn = {1091-6490}, mesh = {Animals ; *Anthropology ; Archaeology ; Europe ; *Extinction, Biological ; Fossils ; Genomics/methods ; Humans ; *Neanderthals ; Radiometric Dating ; }, abstract = {Elucidating when Neanderthal populations disappeared from Eurasia is a key question in paleoanthropology, and Belgium is one of the key regions for studying the Middle to Upper Paleolithic transition. Previous radiocarbon dating placed the Spy Neanderthals among the latest surviving Neanderthals in Northwest Europe with reported dates as young as 23,880 ± 240 B.P. (OxA-8912). Questions were raised, however, regarding the reliability of these dates. Soil contamination and carbon-based conservation products are known to cause problems during the radiocarbon dating of bulk collagen samples. Employing a compound-specific approach that is today the most efficient in removing contamination and ancient genomic analysis, we demonstrate here that previous dates produced on Neanderthal specimens from Spy were inaccurately young by up to 10,000 y due to the presence of unremoved contamination. Our compound-specific radiocarbon dates on the Neanderthals from Spy and those from Engis and Fonds-de-Forêt demonstrate that they disappeared from Northwest Europe at 44,200 to 40,600 cal B.P. (at 95.4% probability), much earlier than previously suggested. Our data contribute significantly to refining models for Neanderthal disappearance in Europe and, more broadly, show that chronometric models regarding the appearance or disappearance of animal or hominin groups should be based only on radiocarbon dates obtained using robust pretreatment methods.}, }
@article {pmid33797824, year = {2021}, author = {Ocobock, C and Lacy, S and Niclou, A}, title = {Between a rock and a cold place: Neanderthal biocultural cold adaptations.}, journal = {Evolutionary anthropology}, volume = {30}, number = {4}, pages = {262-279}, doi = {10.1002/evan.21894}, pmid = {33797824}, issn = {1520-6505}, mesh = {Adaptation, Physiological/*physiology ; Animals ; Anthropology, Physical ; Body Temperature Regulation/physiology ; *Cold Temperature ; Energy Metabolism/physiology ; Female ; Humans ; Male ; Neanderthals/*anatomy &amp; histology/*physiology ; }, abstract = {A large body of work focuses on the unique aspects of Neanderthal anatomy, inferred physiology, and behavior to test the assumption that Neanderthals were hyper-adapted to living in cold environments. This research has expanded over the years to include previously unexplored and potentially adaptive features such as brown adipose tissue and fire-usage. Here we review the current state of knowledge of Neanderthal cold adaptations along morphological, physiological, and behavioral lines. While highlighting foundational as well as recent work, we also emphasize key areas for future research. Despite thriving in a variety of climates, it is well-accepted that Neanderthals appear to be the most cold-adapted of known fossil hominin groups; however, there are still many unknowns. There is a great deal yet to be uncovered about the nature and manifestation of Neanderthal adaptation and how the synergy of biology and culture helped buffer them against extreme and variable environments.}, }
@article {pmid33794419, year = {2021}, author = {Baab, KL and Nesbitt, A and Hublin, JJ and Neubauer, S}, title = {Assessing the status of the KNM-ER 42700 fossil using Homo erectus neurocranial development.}, journal = {Journal of human evolution}, volume = {154}, number = {}, pages = {102980}, doi = {10.1016/j.jhevol.2021.102980}, pmid = {33794419}, issn = {1095-8606}, mesh = {Animals ; Child ; Child, Preschool ; *Fossils ; Hominidae/anatomy &amp; histology/*growth &amp; development ; Humans ; Infant ; Neanderthals/anatomy &amp; histology/growth &amp; development ; Pan troglodytes/anatomy &amp; histology/growth &amp; development ; Phylogeny ; Skull/anatomy &amp; histology/*growth &amp; development ; }, abstract = {Based on ontogenetic data of endocranial shape, it has been proposed that a younger than previously assumed developmental status of the 1.5-Myr-old KNM-ER 42700 calvaria could explain why the calvaria of this fossil does not conform to the shape of other Homo erectus individuals. Here, we investigate (ecto)neurocranial ontogeny in H. erectus and assess the proposed juvenile status of this fossil using recent Homo sapiens, chimpanzees (Pan troglodytes), and Neanderthals (Homo neanderthalensis) to model and discuss changes in neurocranial shape from the juvenile to adult stages. We show that all four species share common patterns of developmental shape change resulting in a relatively lower cranial vault and expanded supraorbital torus at later developmental stages. This finding suggests that ectoneurocranial data from extant hominids can be used to model the ontogenetic trajectory for H. erectus, for which only one well-preserved very young individual is known. However, our study also reveals differences in the magnitudes and, to a lesser extent, directions of the species-specific trajectories that add to the overall shared pattern of neurocranial shape changes. We demonstrate that the very young H. erectus juvenile from Mojokerto together with subadult and adult H. erectus individuals cannot be accommodated within the pattern of the postnatal neurocranial trajectory for humans. Instead, the chimpanzee pattern might be a better 'fit' for H. erectus despite their more distant phylogenetic relatedness. The data are also compatible with an ontogenetic shape trajectory that is in some regards intermediate between that of recent H. sapiens and chimpanzees, implying a unique trajectory for H. erectus that combines elements of both extant species. Based on this new knowledge, neurocranial shape supports the assessment that KNM-ER 42700 is a young juvenile H. erectus if H. erectus followed an ontogenetic shape trajectory that was more similar to chimpanzees than humans.}, }
@article {pmid33791713, year = {2021}, author = {Huffman, J and Butler-Laporte, G and Khan, A and Drivas, TG and Peloso, GM and Nakanishi, T and Verma, A and Kiryluk, K and Richards, JB and Zeberg, H}, title = {Alternative splicing of OAS1 alters the risk for severe COVID-19.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {33791713}, support = {UL1 TR001873/TR/NCATS NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; }, abstract = {A locus containing OAS1/2/3 has been identified as a risk locus for severe COVID-19 among Europeans ancestry individuals, with a protective haplotype of ∼75 kilobases derived from Neanderthals. Here, we show that among several potentially causal variants at this locus, a splice variant of OAS1 occurs in people of African ancestry independently of the Neanderthal haplotype and confers protection against COVID-19 of a magnitude similar to that seen in individuals without African ancestry.}, }
@article {pmid33787889, year = {2021}, author = {Yair, S and Lee, KM and Coop, G}, title = {The timing of human adaptation from Neanderthal introgression.}, journal = {Genetics}, volume = {218}, number = {1}, pages = {}, pmid = {33787889}, issn = {1943-2631}, support = {R01 GM108779/GM/NIGMS NIH HHS/United States ; R01 GM121372/GM/NIGMS NIH HHS/United States ; R35 GM136290/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics/physiology ; Adaptation, Physiological/genetics ; Alleles ; Animals ; Biological Evolution ; Evolution, Molecular ; Gene Frequency/genetics ; Genetic Introgression/*genetics ; Genome, Human/genetics ; Haplotypes/genetics ; Hominidae/*genetics ; Humans ; Neanderthals/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Selection, Genetic/genetics ; }, abstract = {Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long-term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of adaptive Neanderthal introgression. From these, we identify cases in which Neanderthal-introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples.}, }
@article {pmid33774376, year = {2021}, author = {Chevalier, T and Colard, T and Colombo, A and Golovanova, L and Doronichev, V and Hublin, JJ}, title = {Early ontogeny of humeral trabecular bone in Neandertals and recent modern humans.}, journal = {Journal of human evolution}, volume = {154}, number = {}, pages = {102968}, doi = {10.1016/j.jhevol.2021.102968}, pmid = {33774376}, issn = {1095-8606}, mesh = {Adolescent ; Animals ; Cancellous Bone/*growth &amp; development ; Child ; Child, Preschool ; Female ; *Fossils ; Humans ; *Humerus/growth &amp; development ; Infant ; Male ; *Neanderthals ; Pan troglodytes ; }, abstract = {Trabecular bone ontogeny is well known in modern humans and unknown in Neandertals. Yet the bone developmental pattern is useful for interpreting fossils from evolutionary and functional perspectives. Interestingly, microstructure in early ontogeny is supposedly not influenced by high and specific mechanical loading related to the lifestyle of a human group and consequently does not directly depend on the activities of hunter-gatherers. Here, we specifically explored the early growth trajectories of the trabecular bone structure of the humerus and emphasized in particular how bone fraction (bone volume/total volume [BV/TV]) was built up in Neandertals, given the specific modern human bone loss after birth and the use of BV/TV in functional studies. Six Neandertals and 26 recent modern humans ranging from perinates to adolescents were included in this study. Six trabecular parameters were measured within a cubic region of interest extracted from the proximal metaphysis of the humerus. We found that the microstructural changes in Neandertals during early ontogeny (<1 year) fit with modern human growth trajectories for each parameter. The specific bone loss occurring immediately after birth in modern humans also occurred in Neandertals (but not in chimpanzees). However, the early childhood fossil Ferrassie 6 presented unexpectedly high BV/TV, whereas the high BV/TV in the Crouzade I adolescent was predictable. These results suggest that Neandertals and modern humans shared predetermined early growth trajectories and developmental mechanisms. We assume that the close relationship between skeletal characteristics in early ontogeny and adults in modern humans also existed in Neandertals. However, it was difficult to ensure that the high BV/TV in Neandertal early childhood, represented by only one individual, was at the origin of the high BV/TV observed in adults. Consequently, our study does not challenge the mechanical hypothesis that explains the trabecular gracilization of the humerus during the Holocene.}, }
@article {pmid33769498, year = {2021}, author = {Sjödin, P and McKenna, J and Jakobsson, M}, title = {Estimating divergence times from DNA sequences.}, journal = {Genetics}, volume = {217}, number = {4}, pages = {}, pmid = {33769498}, issn = {1943-2631}, mesh = {Animals ; DNA, Ancient ; Genetic Drift ; Humans ; *Mutation Rate ; Neanderthals/genetics ; *Polymorphism, Genetic ; Population/*genetics ; Time ; }, abstract = {The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the "Two-Two (TT)" and the "Two-Two-outgroup (TTo)" methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.}, }
@article {pmid33753899, year = {2021}, author = {Teixeira, JC and Jacobs, GS and Stringer, C and Tuke, J and Hudjashov, G and Purnomo, GA and Sudoyo, H and Cox, MP and Tobler, R and Turney, CSM and Cooper, A and Helgen, KM}, title = {Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {5}, pages = {616-624}, pmid = {33753899}, issn = {2397-334X}, mesh = {Animals ; Asia, Southeastern ; Fossils ; *Hominidae/genetics ; Humans ; Islands ; *Neanderthals ; }, abstract = {The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.}, }
@article {pmid33707474, year = {2021}, author = {Mayoral, E and Díaz-Martínez, I and Duveau, J and Santos, A and Ramírez, AR and Morales, JA and Morales, LA and Díaz-Delgado, R}, title = {Tracking late Pleistocene Neandertals on the Iberian coast.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4103}, pmid = {33707474}, issn = {2045-2322}, abstract = {Here, we report the recent discovery of 87 Neandertal footprints on the Southwest of the Iberian Peninsula (Doñana shoreline, Spain) located on an upper Pleistocene aeolian littoral setting (about 106 ± 19 kyr). Morphometric comparisons, high resolution digital photogrammetric 3D models and detailed sedimentary analysis have been provided to characterized the footprints and the palaeoenvironment. The footprints were impressed in the shoreline of a hypersaline swamped area related to benthic microbial mats, close to the coastline. They have a rounded heel, a longitudinal arch, relatively short toes, and adducted hallux, and represent the oldest upper Pleistocene record of Neandertal footprints in the world. Among these 87 footprints, 31 are longitudinally complete and measure from 14 to 29 cm. The calculated statures range from 104 to 188 cm, with half of the data between 130 and 150 cm. The wide range of sizes of the footprints suggests the existence of a social group integrated by individuals of different age classes but dominated, however, by non-adult individuals. The footprints, which are outside the flooded area are oriented perpendicular to the shoreline. These 87 footprints reinforce the ecological scenario of Neandertal groups established in coastal areas.}, }
@article {pmid33707343, year = {2021}, author = {García-Campos, C and Martinén-Torres, M and Modesto-Mata, M and Martín-Francés, L and Martínez de Pinillos, M and Bermúdez de Castro, JM}, title = {Indicators of sexual dimorphism in Homo antecessor permanent canines.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {99}, number = {}, pages = {1-18}, doi = {10.4436/JASS.99001}, pmid = {33707343}, issn = {2037-0644}, abstract = {One of the main concerns of paleoanthropologists is to make a correct interpretation of the variability observed in the fossil record. However, the current knowledge about sexual dimorphism in the human lineage comes mainly from the study of modern human, Neanderthal and pre-Neanderthal populations, whereas information available about the intrapopulation variability of the groups that preceded these taxa is still ambiguous. In this preliminary study, Homo antecessor dental sample was assessed with the aim of trying to evaluate the degree of variability of their permanent canines` dental tissue proportions. Microtomographic techniques were here employed in order to measure and compare the crown volumes and surface areas of their enamel caps and dentine-pulp complexes. Then, the Pearson`s Coefficient of Variation and the Euclidean Distance were assessed to evaluate of intrapopulation variability of Gran Dolina TD6.2 dental sample. The values obtained were also compared with those of the dental samples from Sima de los Huesos site (Spain), the Neanderthal site of Krapina (Croatia), as well as from a broad forensic collection of known sex. Our results showed a marked intrapopulation variability in the dental tissues measurements of the canines of the individuals H1 and H3 from this site. This variability may be interpreted as an indicator of sexual dimorphism. If this is the case, H1 may be considered as a male individual, whereas H3 would be a female. Future discoveries of new fossils in the level TD6.2 of Gran Dolina site might help to confirm or refute this hypothesis.}, }
@article {pmid33674720, year = {2021}, author = {Banks, WE and Moncel, MH and Raynal, JP and Cobos, ME and Romero-Alvarez, D and Woillez, MN and Faivre, JP and Gravina, B and d'Errico, F and Locht, JL and Santos, F}, title = {An ecological niche shift for Neanderthal populations in Western Europe 70,000 years ago.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5346}, pmid = {33674720}, issn = {2045-2322}, abstract = {Middle Paleolithic Neanderthal populations occupied Eurasia for at least 250,000 years prior to the arrival of anatomically modern humans. While a considerable body of archaeological research has focused on Neanderthal material culture and subsistence strategies, little attention has been paid to the relationship between regionally specific cultural trajectories and their associated existing fundamental ecological niches, nor to how the latter varied across periods of climatic variability. We examine the Middle Paleolithic archaeological record of a naturally constrained region of Western Europe between 82,000 and 60,000 years ago using ecological niche modeling methods. Evaluations of ecological niche estimations, in both geographic and environmental dimensions, indicate that 70,000 years ago the range of suitable habitats exploited by these Neanderthal populations contracted and shifted. These ecological niche dynamics are the result of groups continuing to occupy habitual territories that were characterized by new environmental conditions during Marine Isotope Stage 4. The development of original cultural adaptations permitted this territorial stability.}, }
@article {pmid33649543, year = {2021}, author = {Conde-Valverde, M and Martínez, I and Quam, RM and Rosa, M and Velez, AD and Lorenzo, C and Jarabo, P and Bermúdez de Castro, JM and Carbonell, E and Arsuaga, JL}, title = {Neanderthals and Homo sapiens had similar auditory and speech capacities.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {5}, pages = {609-615}, pmid = {33649543}, issn = {2397-334X}, mesh = {Animals ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; Speech ; }, abstract = {The study of audition in fossil hominins is of great interest given its relationship with intraspecific vocal communication. While the auditory capacities have been studied in early hominins and in the Middle Pleistocene Sima de los Huesos hominins, less is known about the hearing abilities of the Neanderthals. Here, we provide a detailed approach to their auditory capacities. Relying on computerized tomography scans and a comprehensive model from the field of auditory bioengineering, we have established sound power transmission through the outer and middle ear and calculated the occupied bandwidth in Neanderthals. The occupied bandwidth is directly related to the efficiency of the vocal communication system of a species. Our results show that the occupied bandwidth of Neanderthals was greater than the Sima de los Huesos hominins and similar to extant humans, implying that Neanderthals evolved the auditory capacities to support a vocal communication system as efficient as modern human speech.}, }
@article {pmid33649483, year = {2021}, author = {Vaesen, K and Dusseldorp, GL and Brandt, MJ}, title = {An emerging consensus in palaeoanthropology: demography was the main factor responsible for the disappearance of Neanderthals.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4925}, pmid = {33649483}, issn = {2045-2322}, abstract = {The causes of Neanderthal disappearance about 40,000 years ago remain highly contested. Over a dozen serious hypotheses are currently endorsed to explain this enigmatic event. Given the relatively large number of contending explanations and the relatively large number of participants in the debate, it is unclear how strongly each contender is supported by the research community. What does the community actually believe about the demise of Neanderthals? To address this question, we conducted a survey among practicing palaeo-anthropologists (total number of respondents = 216). It appears that received wisdom is that demography was the principal cause of the demise of Neanderthals. In contrast, there is no received wisdom about the role that environmental factors and competition with modern humans played in the extinction process; the research community is deeply divided about these issues. Finally, we tested the hypothesis that palaeo-anthropologists' stand in the debate co-varies with their socio-political views and attitudes. We found no evidence for such a correlation.}, }
@article {pmid33644865, year = {2021}, author = {Richards, GD and Guipert, G and Jabbour, RS and Defleur, AR}, title = {Neanderthal cranial remains from Baume Moula-Guercy (Soyons, Ardèche, France).}, journal = {American journal of physical anthropology}, volume = {175}, number = {1}, pages = {201-226}, doi = {10.1002/ajpa.24256}, pmid = {33644865}, issn = {1096-8644}, mesh = {Adult ; Animals ; Anthropology, Physical ; Female ; France ; Humans ; Male ; Neanderthals/*anatomy &amp; histology ; Skull/*anatomy &amp; histology ; }, abstract = {OBJECTIVES: We provide the first comparative description of the Guercy 1 cranium and isolated cranial fragments from Baume Moula-Guercy and examine their affinities to European Preneanderthals, Neanderthals, and Homo sapiens.<br><br>MATERIALS AND METHODS: The Moula-Guercy hominins derive from deposits chronostratigraphically and biostratigraphically dated to the Eemian Interglacial (MIS 5e). For comparisons we compiled a sample of European and Southwest Asian subadult-adult Middle-to-Late Pleistocene hominins (&#x2248;MIS 14-MIS 2; N = 184). This sample represents a Preneanderthal-Neanderthal group and a H. sapiens group, both of which were further divided into three time-successive subgroups defined by associated marine isotope stages (MIS). Metric and morphological observations were made on the original fossils and a virtual reconstruction of Guercy 1. Developmental age and sex and the minimum-maximum number of individuals were assessed.<br><br>RESULTS: Guercy 1 represents the remains of a late stage adolescent (&#x2248;15-16.0&#x2009;years) female. Morphological and metric data combine to associate the total morphological pattern expressed in Guercy 1 with our MIS 7-MIS 5e ("Early Neanderthal") subgroup. Some features, especially those related to the frontal, suggest linkage to a paleodeme comprising the Moula-Guercy, Artenac, La Chaise Abri Suard and, possibly, the Biache-Saint-Vaast samples.<br><br>DISCUSSION: Remains of MIS 7-MIS 5e Neanderthals are rare and fragmentary, especially those dated to the Last Interglacial. The Baume Moula-Guercy sample provides new insights into the total morphological pattern expressed in MIS 5e Neanderthals. Further, our results support earlier suggestions that MIS 7-MIS 5e European hominins represent a morphotype that is distinct from both earlier and later members of the Preneanderthal-Neanderthal group.}, }
@article {pmid33638923, year = {2022}, author = {Mora-Bermúdez, F and Taverna, E and Huttner, WB}, title = {From stem and progenitor cells to neurons in the developing neocortex: key differences among hominids.}, journal = {The FEBS journal}, volume = {289}, number = {6}, pages = {1524-1535}, doi = {10.1111/febs.15793}, pmid = {33638923}, issn = {1742-4658}, mesh = {Animals ; *Hominidae ; *Neocortex/physiology ; *Neural Stem Cells ; Neurogenesis ; Neurons ; }, abstract = {Comparing the biology of humans to that of other primates, and notably other hominids, is a useful path to learn more about what makes us human. Some of the most interesting differences among hominids are closely related to brain development and function, for example behaviour and cognition. This makes it particularly interesting to compare the hominid neural cells of the neocortex, a part of the brain that plays central roles in those processes. However, well-preserved tissue from great apes is usually extremely difficult to obtain. A variety of new alternative tools, for example brain organoids, are now beginning to make it possible to search for such differences and analyse their potential biological and biomedical meaning. Here, we present an overview of recent findings from comparisons of the neural stem and progenitor cells (NSPCs) and neurons of hominids. In addition to differences in proliferation and differentiation of NSPCs, and maturation of neurons, we highlight that the regulation of the timing of these processes is emerging as a general foundational difference in the development of the neocortex of hominids.}, }
@article {pmid33633408, year = {2021}, author = {Zhou, S and Butler-Laporte, G and Nakanishi, T and Morrison, DR and Afilalo, J and Afilalo, M and Laurent, L and Pietzner, M and Kerrison, N and Zhao, K and Brunet-Ratnasingham, E and Henry, D and Kimchi, N and Afrasiabi, Z and Rezk, N and Bouab, M and Petitjean, L and Guzman, C and Xue, X and Tselios, C and Vulesevic, B and Adeleye, O and Abdullah, T and Almamlouk, N and Chen, Y and Chassé, M and Durand, M and Paterson, C and Normark, J and Frithiof, R and Lipcsey, M and Hultström, M and Greenwood, CMT and Zeberg, H and Langenberg, C and Thysell, E and Pollak, M and Mooser, V and Forgetta, V and Kaufmann, DE and Richards, JB}, title = {A Neanderthal OAS1 isoform protects individuals of European ancestry against COVID-19 susceptibility and severity.}, journal = {Nature medicine}, volume = {27}, number = {4}, pages = {659-667}, pmid = {33633408}, issn = {1546-170X}, support = {MC_UU_00006/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {2',5'-Oligoadenylate Synthetase/genetics/*physiology ; Aged ; Aged, 80 and over ; Animals ; COVID-19/*etiology/genetics ; Case-Control Studies ; Female ; *Genetic Predisposition to Disease ; Humans ; Interleukin-10 Receptor beta Subunit/genetics ; Male ; Mendelian Randomization Analysis ; Middle Aged ; Neanderthals ; Protein Isoforms/physiology ; Quantitative Trait Loci ; *SARS-CoV-2 ; Severity of Illness Index ; Whites ; }, abstract = {To identify circulating proteins influencing Coronavirus Disease 2019 (COVID-19) susceptibility and severity, we undertook a two-sample Mendelian randomization (MR) study, rapidly scanning hundreds of circulating proteins while reducing bias due to reverse causation and confounding. In up to 14,134 cases and 1.2 million controls, we found that an s.d. increase in OAS1 levels was associated with reduced COVID-19 death or ventilation (odds ratio (OR) = 0.54, P = 7 × 10[-8]), hospitalization (OR = 0.61, P = 8 × 10[-8]) and susceptibility (OR = 0.78, P = 8 × 10[-6]). Measuring OAS1 levels in 504 individuals, we found that higher plasma OAS1 levels in a non-infectious state were associated with reduced COVID-19 susceptibility and severity. Further analyses suggested that a Neanderthal isoform of OAS1 in individuals of European ancestry affords this protection. Thus, evidence from MR and a case-control study support a protective role for OAS1 in COVID-19 adverse outcomes. Available pharmacological agents that increase OAS1 levels could be prioritized for drug development.}, }
@article {pmid33620372, year = {2021}, author = {Baldoni, M and Al-Hashmi, M and Bianchi, AE and Sakal, F and Al-Naimi, F and Leisten, T and Martínez-Labarga, C and Tomei, S}, title = {Bioarchaeology-related studies in the Arabian Gulf: potentialities and shortcomings.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {72}, number = {1}, pages = {17-32}, doi = {10.1127/homo/2021/1282}, pmid = {33620372}, issn = {1618-1301}, mesh = {Animals ; *Archaeology ; Human Migration ; Humans ; *Neanderthals/genetics ; }, abstract = {Archaeological studies provide a powerful tool to understand the prehistoric societies, especially when combined to cutting-edge morphological and molecular anthropological analyses, allowing reconstructing past population dynamics, admixture events, and socio-cultural changes. Despite the advances achieved in the last decades by archaeological studies worldwide, several regions of the World have been spared from this scientific improvement due to various reasons. The Arabian Gulf represents a unique ground to investigate, being the passageway for human migrations and one of the hypothesized areas in which Neanderthal introgression occurred. A number of archaeological sites are currently present in the Arabian Gulf and have witnessed the antiquity and the intensiveness of the human settlements in the region. Nevertheless, the archaeological and anthropological investigation in the Gulf is still in its infancy. Data collected through archaeological studies in the area have the potential to help answering adamant questions of human history from the beginning of the structuring of genetic diversity in human species to the Neolithisation process. This review aims at providing an overview of the archaeological studies in the Arabian Gulf with special focus to Qatar, highlighting potentialities and shortcomings.}, }
@article {pmid33619340, year = {2021}, author = {Zilio, L and Hammond, H and Karampaglidis, T and Sánchez-Romero, L and Blasco, R and Rivals, F and Rufà, A and Picin, A and Chacón, MG and Demuro, M and Arnold, LJ and Rosell, J}, title = {Examining Neanderthal and carnivore occupations of Teixoneres Cave (Moià, Barcelona, Spain) using archaeostratigraphic and intra-site spatial analysis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4339}, pmid = {33619340}, issn = {2045-2322}, abstract = {Teixoneres Cave (Moià, Barcelona, Spain) is a reference site for Middle Palaeolithic studies of the Iberian Peninsula. The cave preserves an extensive stratigraphic sequence made up of eight units, which is presented in depth in this work. The main goal of this study is to undertake an initial spatial examination of Unit III, formed during Marine Isotope Stage 3, with the aim of understanding spatial organization and past activities developed by Neanderthals and carnivores (bears, hyenas and smaller carnivores). The total sample analysed includes 38,244 archaeological items and 5888 limestone blocks. The application of GIS tools allows us to clearly distinguish three geologically-defined stratigraphic subunits. Unit III has been previously interpreted as a palimpsest resulting from alternating occupation of the cave by human groups and carnivores. The distribution study shows that faunal specimens, lithic artefacts, hearths and charcoal fragments are significantly concentrated at the entrance of the cave where, it is inferred, hominins carried out different activities, while carnivores preferred the sheltered zones in the inner areas of the cave. The results obtained reveal a spatial pattern characterized by fire use related zones, and show that the site was occupied by Neanderthals in a similar and consistent way throughout the ˃ 7000 years range covered by the analysed subunits. This spatial pattern is interpreted as resulting from repeated short-term human occupations.}, }
@article {pmid33616898, year = {2021}, author = {González-Urquijo, J and Bailey, SE and Lazuen, T}, title = {Axlor's level IV human remains are convincingly Neanderthals: A reply to Gómez-Olivencia et al.}, journal = {American journal of physical anthropology}, volume = {176}, number = {4}, pages = {553-558}, doi = {10.1002/ajpa.24252}, pmid = {33616898}, issn = {1096-8644}, mesh = {Animals ; Body Remains ; Humans ; *Neanderthals ; }, }
@article {pmid33595856, year = {2021}, author = {Lee, JW and Lee, IH and Sato, T and Kong, SW and Iimura, T}, title = {Genetic variation analyses indicate conserved SARS-CoV-2-host interaction and varied genetic adaptation in immune response factors in modern human evolution.}, journal = {Development, growth &amp; differentiation}, volume = {63}, number = {3}, pages = {219-227}, pmid = {33595856}, issn = {1440-169X}, support = {U01 TR002623/TR/NCATS NIH HHS/United States ; R01 MH107205/MH/NIMH NIH HHS/United States ; R24 OD024622/OD/NIH HHS/United States ; }, mesh = {*Adaptive Immunity/genetics/immunology ; Animals ; *COVID-19/epidemiology/genetics/immunology ; Conserved Sequence ; *Evolution, Molecular ; *Genetic Variation ; Genome-Wide Association Study ; Host Adaptation/genetics/immunology ; *Host-Pathogen Interactions/genetics/immunology ; Humans ; Pandemics ; SARS-CoV-2/*genetics/immunology ; Sequence Analysis, RNA ; }, abstract = {Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic as of early 2020. Upon infection, SARS-CoV-2 attaches to its receptor, that is, angiotensin-converting enzyme 2 (ACE2), on the surface of host cells and is then internalized into host cells via enzymatic machineries. This subsequently stimulates immune response factors. Since the host immune response and severity of COVID-19 vary among individuals, genetic risk factors for severe COVID-19 cases have been investigated. Our research group recently conducted a survey of genetic variants among SARS-CoV-2-interacting molecules across populations, noting near absence of difference in allele frequency spectrum between populations in these genes. Recent genome-wide association studies have identified genetic risk factors for severe COVID-19 cases in a segment of chromosome 3 that involves six genes encoding three immune-regulatory chemokine receptors and another three molecules. The risk haplotype seemed to be inherited from Neanderthals, suggesting genetic adaptation against pathogens in modern human evolution. Therefore, SARS-CoV-2 uses highly conserved molecules as its virion interaction, whereas its immune response appears to be genetically biased in individuals to some extent. We herein review the molecular process of SARS-CoV-2 infection as well as our further survey of genetic variants of its related immune effectors. We also discuss aspects of modern human evolution.}, }
@article {pmid33593941, year = {2021}, author = {Zeberg, H and Pääbo, S}, title = {A genomic region associated with protection against severe COVID-19 is inherited from Neandertals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {9}, pages = {}, pmid = {33593941}, issn = {1091-6490}, mesh = {Animals ; COVID-19/*genetics/immunology ; Chromosomes, Human, Pair 12/*genetics ; *Evolution, Molecular ; *Genetic Predisposition to Disease ; Haplotypes ; Humans ; Neanderthals/*genetics ; Quantitative Trait Loci ; }, abstract = {It was recently shown that the major genetic risk factor associated with becoming severely ill with COVID-19 when infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is inherited from Neandertals. New, larger genetic association studies now allow additional genetic risk factors to be discovered. Using data from the Genetics of Mortality in Critical Care (GenOMICC) consortium, we show that a haplotype at a region on chromosome 12 associated with requiring intensive care when infected with the virus is inherited from Neandertals. This region encodes proteins that activate enzymes that are important during infections with RNA viruses. In contrast to the previously described Neandertal haplotype that increases the risk for severe COVID-19, this Neandertal haplotype is protective against severe disease. It also differs from the risk haplotype in that it has a more moderate effect and occurs at substantial frequencies in all regions of the world outside Africa. Among ancient human genomes in western Eurasia, the frequency of the protective Neandertal haplotype may have increased between 20,000 and 10,000 y ago and again during the past 1,000 y.}, }
@article {pmid33589653, year = {2021}, author = {Blinkhorn, J and Zanolli, C and Compton, T and Groucutt, HS and Scerri, EML and Crété, L and Stringer, C and Petraglia, MD and Blockley, S}, title = {Nubian Levallois technology associated with southernmost Neanderthals.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2869}, pmid = {33589653}, issn = {2045-2322}, abstract = {Neanderthals occurred widely across north Eurasian landscapes, but between ~ 70 and 50 thousand years ago (ka) they expanded southwards into the Levant, which had previously been inhabited by Homo sapiens. Palaeoanthropological research in the first half of the twentieth century demonstrated alternate occupations of the Levant by Neanderthal and Homo sapiens populations, yet key early findings have largely been overlooked in later studies. Here, we present the results of new examinations of both the fossil and archaeological collections from Shukbah Cave, located in the Palestinian West Bank, presenting new quantitative analyses of a hominin lower first molar and associated stone tool assemblage. The hominin tooth shows clear Neanderthal affinities, making it the southernmost known fossil specimen of this population/species. The associated Middle Palaeolithic stone tool assemblage is dominated by Levallois reduction methods, including the presence of Nubian Levallois points and cores. This is the first direct association between Neanderthals and Nubian Levallois technology, demonstrating that this stone tool technology should not be considered an exclusive marker of Homo sapiens.}, }
@article {pmid33584703, year = {2020}, author = {Bach, JF}, title = {Revisiting the Hygiene Hypothesis in the Context of Autoimmunity.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {615192}, pmid = {33584703}, issn = {1664-3224}, mesh = {Animals ; Autoimmune Diseases/etiology/genetics/immunology/prevention &amp; control ; *Autoimmunity ; Bacteria/immunology ; Biological Evolution ; Causality ; Child ; Cytokines/physiology ; Disease Models, Animal ; Dysbiosis/complications ; Environmental Exposure ; Epidemiologic Methods ; Gastrointestinal Microbiome/immunology ; Host-Pathogen Interactions/immunology ; Humans ; *Hygiene Hypothesis ; Hypersensitivity/etiology/genetics/immunology/prevention &amp; control ; Immunity, Innate ; Neanderthals/genetics/immunology ; Parasites/immunology ; Stochastic Processes ; *Symbiosis ; Toll-Like Receptors/physiology ; Viruses/immunology ; }, abstract = {Initially described for allergic diseases, the hygiene hypothesis was extended to autoimmune diseases in the early 2000s. A historical overview allows appreciation of the development of this concept over the last two decades and its discussion in the context of evolution. While the epidemiological data are convergent, with a few exceptions, the underlying mechanisms are multiple and complex. A major question is to determine what is the respective role of pathogens, bacteria, viruses, and parasites, versus commensals. The role of the intestinal microbiota has elicited much interest, but is it a cause or a consequence of autoimmune-mediated inflammation? Our hypothesis is that both pathogens and commensals intervene. Another question is to dissect what are the underlying cellular and molecular mechanisms. The role of immunoregulatory cytokines, in particular interleukin-10 and TGF beta is probably essential. An important place should also be given to ligands of innate immunity receptors present in bacteria, viruses or parasites acting independently of their immunogenicity. The role of Toll-Like Receptor (TLR) ligands is well documented including via TLR ligand desensitization.}, }
@article {pmid33574596, year = {2021}, author = {Remmel, A}, title = {Neanderthal-like 'mini-brains' created in lab with CRISPR.}, journal = {Nature}, volume = {590}, number = {7846}, pages = {376-377}, pmid = {33574596}, issn = {1476-4687}, mesh = {Brain ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA ; Humans ; *Neanderthals/genetics ; Stem Cells ; }, }
@article {pmid33574182, year = {2021}, author = {Trujillo, CA and Rice, ES and Schaefer, NK and Chaim, IA and Wheeler, EC and Madrigal, AA and Buchanan, J and Preissl, S and Wang, A and Negraes, PD and Szeto, RA and Herai, RH and Huseynov, A and Ferraz, MSA and Borges, FS and Kihara, AH and Byrne, A and Marin, M and Vollmers, C and Brooks, AN and Lautz, JD and Semendeferi, K and Shapiro, B and Yeo, GW and Smith, SEP and Green, RE and Muotri, AR}, title = {Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment.}, journal = {Science (New York, N.Y.)}, volume = {371}, number = {6530}, pages = {}, pmid = {33574182}, issn = {1095-9203}, support = {R35 GM133569/GM/NIGMS NIH HHS/United States ; R01 HL137223/HL/NHLBI NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; R01 MH121487/MH/NIMH NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; R01 HG004659/HG/NHGRI NIH HHS/United States ; R01 MH113545/MH/NIMH NIH HHS/United States ; K01 AA026911/AA/NIAAA NIH HHS/United States ; U19 MH107367/MH/NIMH NIH HHS/United States ; T32 HG008345/HG/NHGRI NIH HHS/United States ; U41 HG009889/HG/NHGRI NIH HHS/United States ; }, mesh = {Alleles ; Alternative Splicing ; Amino Acid Substitution ; Animals ; Binding Sites ; Biological Evolution ; CRISPR-Cas Systems ; Cell Proliferation ; Cerebral Cortex/cytology/*growth &amp; development/*physiology ; Gene Expression Regulation, Developmental ; Genetic Variation ; Genome ; Genome, Human ; Haplotypes ; Hominidae/genetics ; Humans ; Induced Pluripotent Stem Cells ; Neanderthals/*genetics ; Nerve Net/physiology ; Nerve Tissue Proteins/genetics/metabolism ; Neuro-Oncological Ventral Antigen ; Neurons/*physiology ; Organoids ; RNA-Binding Proteins/*genetics/*metabolism ; Synapses/physiology ; }, abstract = {The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (NOVA1) plays a key role in neural development and function. NOVA1 also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of NOVA1 Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in NOVA1, which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species' evolution.}, }
@article {pmid33568824, year = {2021}, author = {Bergström, A and Stringer, C and Hajdinjak, M and Scerri, EML and Skoglund, P}, title = {Origins of modern human ancestry.}, journal = {Nature}, volume = {590}, number = {7845}, pages = {229-237}, pmid = {33568824}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; /WT_/Wellcome Trust/United Kingdom ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa/ethnology ; Animals ; Fossils ; Gene Flow/genetics ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals/genetics ; *Pedigree ; }, abstract = {New finds in the palaeoanthropological and genomic records have changed our view of the origins of modern human ancestry. Here we review our current understanding of how the ancestry of modern humans around the globe can be traced into the deep past, and which ancestors it passes through during our journey back in time. We identify three key phases that are surrounded by major questions, and which will be at the frontiers of future research. The most recent phase comprises the worldwide expansion of modern humans between 40 and 60 thousand years ago (ka) and their last known contacts with archaic groups such as Neanderthals and Denisovans. The second phase is associated with a broadly construed African origin of modern human diversity between 60 and 300 ka. The oldest phase comprises the complex separation of modern human ancestors from archaic human groups from 0.3 to 1 million years ago. We argue that no specific point in time can currently be identified at which modern human ancestry was confined to a limited birthplace, and that patterns of the first appearance of anatomical or behavioural traits that are used to define Homo sapiens are consistent with a range of evolutionary histories.}, }
@article {pmid33564646, year = {2021}, author = {Mortazavi, SAR and Kaveh-Ahangar, K and Mortazavi, SMJ and Firoozi, D and Haghani, M}, title = {How Our Neanderthal Genes Affect the COVID-19 Mortality: Iran and Mongolia, Two Countries with the Same SARS-CoV-2 Mutation Cluster but Different Mortality Rates.}, journal = {Journal of biomedical physics &amp; engineering}, volume = {11}, number = {1}, pages = {109-114}, pmid = {33564646}, issn = {2251-7200}, abstract = {Neanderthal genes possibly gave modern human protection against viruses. However, a recent study revealed that that a long sequence of DNA that is inherited from our Neanderthal ancestors can be linked to severe COVID-19 infection and hospitalization. Substantial evidence now indicates that our genetic background may be involved in the transmissibility of SARS-CoV-2 and the rapid progress of COVID-19 in some infected individuals. Although both morbidity and mortality of COVID-19 strongly depends on key factors such as age and co-existing health conditions, potential classes of human genomic variants possibly affect the likelihood of SARS-CoV-2 infection and its progress. Despite Iran and Mongolia seem to share the same SARS-CoV-2 mutation cluster, the COVID-19 mortality rates in these two countries are drastically different. While the population in Iran is 25.8 times higher than that of Mongolia, the number of confirmed cases is 1170 times higher. Moreover, the death rate shows a drastic difference. Since Neanderthals interbred with modern humans in Middle East between 47,000 and 65,000 years ago before going extinct 40,000 years ago, some Iranians have much more Neanderthal DNA than other people. Although neither genetic background nor environmental factors alone can determine our risk of developing severe COVID-19, our genes clearly affect both the development and progression of infectious diseases including COVID-19. Given these considerations, we believe that these great differences, at least to some extent, can be due to the proportion of Neanderthal genes among the people of these two countries.}, }
@article {pmid33556445, year = {2021}, author = {Reinscheid, RK and Mafessoni, F and Lüttjohann, A and Jüngling, K and Pape, HC and Schulz, S}, title = {Neandertal introgression and accumulation of hypomorphic mutations in the neuropeptide S (NPS) system promote attenuated functionality.}, journal = {Peptides}, volume = {138}, number = {}, pages = {170506}, doi = {10.1016/j.peptides.2021.170506}, pmid = {33556445}, issn = {1873-5169}, mesh = {Animals ; *Biological Evolution ; Genetic Introgression/*genetics ; Hominidae/genetics ; Humans ; Mutation/genetics ; Neanderthals/genetics ; Neuropeptides/genetics ; Polymorphism, Single Nucleotide/genetics ; Receptors, G-Protein-Coupled/*genetics ; *Selection, Genetic ; }, abstract = {The neuropeptide S (NPS) system plays an important role in fear and fear memory processing but has also been associated with allergic and inflammatory diseases. Genes for NPS and its receptor NPSR1 are found in all tetrapods. Compared to non-human primates, several non-synonymous single-nucleotide polymorphisms (SNPs) occur in both human genes that collectively result in functional attenuation, suggesting adaptive mechanisms in a human context. To investigate historic and geographic origins of these hypomorphic mutations and explore genetic signs of selection, we analyzed ancient genomes and worldwide genotype frequencies of four prototypic SNPs in the NPS system. Neandertal and Denisovan genomes contain exclusively ancestral alleles for NPSR1 while all derived alleles occur in ancient genomes of anatomically modern humans, indicating that they arose in modern Homo sapiens. Worldwide genotype frequencies for three hypomorphic NPSR1 SNPs show significant regional homogeneity but follow a gradient towards increasing derived allele frequencies that supports an out-of-Africa scenario. Increased density of high-frequency polymorphisms around the three NPSR1 loci suggests weak or possibly balancing selection. A hypomorphic mutation in the NPS precursor, however, was detected at high frequency in Eurasian Neandertal genomes and shows genetic signatures indicating that it was introgressed into the human gene pool, particularly in Southern Europe, by interbreeding with Neandertals. We discuss potential evolutionary scenarios including behavior and immune-based natural selection.}, }
@article {pmid33547403, year = {2021}, author = {Rampelli, S and Turroni, S and Mallol, C and Hernandez, C and Galván, B and Sistiaga, A and Biagi, E and Astolfi, A and Brigidi, P and Benazzi, S and Lewis, CM and Warinner, C and Hofman, CA and Schnorr, SL and Candela, M}, title = {Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {169}, pmid = {33547403}, issn = {2399-3642}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Archaeology ; DNA, Ancient/isolation &amp; purification ; Ecosystem ; Feces/*microbiology ; Fossils/microbiology ; *Gastrointestinal Microbiome ; Geologic Sediments/analysis/microbiology ; History, Ancient ; Humans ; Metagenomics ; Neanderthals/*microbiology ; Sequence Analysis, DNA ; Spain ; }, abstract = {A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.}, }
@article {pmid33543780, year = {2021}, author = {Selig, KR and Kupczik, K and Silcox, MT}, title = {The effect of high wear diets on the relative pulp volume of the lower molars.}, journal = {American journal of physical anthropology}, volume = {174}, number = {4}, pages = {804-811}, doi = {10.1002/ajpa.24242}, pmid = {33543780}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; *Dental Pulp/anatomy &amp; histology/physiology ; Diet/*veterinary ; *Hominidae/anatomy &amp; histology/physiology ; Molar/anatomy &amp; histology/physiology ; Tooth Wear/*pathology ; }, abstract = {OBJECTIVES: One role of dental pulp is in the upkeep and maintenance of dentine. Under wear, odontoblasts in the pulp deposit tertiary dentine to ensure the sensitive internal dental tissues are not exposed and vulnerable to infection. It follows that there may be an adaptive advantage for increasing molar pulp volume in anthropoid primate taxa that are prone to high levels of wear. The relative volume of dental pulp is therefore predicted to covary with dietary abrasiveness (in the sense of including foods that cause high degrees of wear).<br><br>MATERIALS AND METHODS: We examined relatively unworn lower second molars in pairs of species of extant hominoids, cebids, and pitheciids that vary in the abrasiveness of their diet (n = 36). Using micro-CT scans, we measured the percent of tooth that is pulp (PTP) as the ratio of pulp volume to that of the total volume of the tooth.<br><br>RESULTS: We found that in each pair of species, the taxa that consume a more abrasive diet had a significantly higher PTP than the closely related taxa that consume a softer diet.<br><br>CONCLUSIONS: Our results point to an adaptive mechanism in the molars of taxa that consume abrasive diets and are thus subject to higher levels of wear. Our results provide additional understanding of the relationship between dental pulp and diet and may offer insight into the diet of extinct taxa such as Paranthropus boisei or into the adaptive context of the taurodont molars of Neanderthals.}, }
@article {pmid33524842, year = {2021}, author = {Lacy, SA}, title = {Evidence of dental agenesis in late pleistocene Homo.}, journal = {International journal of paleopathology}, volume = {32}, number = {}, pages = {103-110}, doi = {10.1016/j.ijpp.2021.01.001}, pmid = {33524842}, issn = {1879-9825}, mesh = {Animals ; *Anodontia ; *Hominidae ; Humans ; Molar, Third/diagnostic imaging ; }, abstract = {OBJECTIVE: Differential diagnosis and tabulation of cases of dental agenesis in Middle and Upper Paleolithic Western Eurasian humans to synthesize this data and to test previous hypotheses about when recent human patterns of third molar agenesis were established.<br><br>MATERIALS: 139 Late Pleistocene human remains and 149 individuals from three Epi-Paleolithic/ Holocene non-agricultural comparative collections.<br><br>METHODS: All remains were visually and radiographically recorded by the author.<br><br>RESULTS: In addition to establishing that third molar agenesis was common during the Late Upper Paleolithic (22,500-10,000 years BP), this study suggests a pattern of increasing prevalence through time.<br><br>CONCLUSIONS: An increase in the prevalence of third molar agenesis in the Late Upper Paleolithic could indicate selection for dental size reduction and orthognathy, but also bio-cultural changes from more intensive food preparation techniques.<br><br>SIGNIFICANCE: Third molar agenesis, a well-known developmental defect, is often reported for recent human skeletal collections, but the prevalence of the condition for Pleistocene hominins had not been previously quantified in order to consider patterns through time. Hypotheses posited for the high prevalence of third molar agenesis, or hypodontia in general, in some recent human groups require an understanding of the prevalence of these traits in the past.<br><br>LIMITATIONS: Paleolithic skeletal remains are incomplete, so these values are under-estimations. Individuals are also separated diachronically and geographically and should not be assumed to represent a single population sample.<br><br>Hypotheses on some of the potential selective forces acting on dental size reduction and subsequent agenesis could be tested in recent humans.}, }
@article {pmid33517134, year = {2021}, author = {Compton, T and Skinner, MM and Humphrey, L and Pope, M and Bates, M and Davies, TW and Parfitt, SA and Plummer, WP and Scott, B and Shaw, A and Stringer, C}, title = {The morphology of the Late Pleistocene hominin remains from the site of La Cotte de St Brelade, Jersey (Channel Islands).}, journal = {Journal of human evolution}, volume = {152}, number = {}, pages = {102939}, doi = {10.1016/j.jhevol.2020.102939}, pmid = {33517134}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Channel Islands ; Female ; Fossils/*anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Paleodontology ; Tooth/*anatomy &amp; histology ; }, abstract = {Thirteen permanent fully erupted teeth were excavated at the Paleolithic site of La Cotte de St Brelade in Jersey in 1910 and 1911. These were all found in the same location, on a ledge behind a hearth in a Mousterian occupation level. They were originally identified as being Neanderthal. A fragment of occipital bone was found in a separate locality in a later season. Recent dating of adjacent sediments gives a probable age of <48 ka. The purpose of this article is to provide an updated description of the morphology of this material and consider its likely taxonomic assignment from comparison with Neanderthal and Homo sapiens samples. One of the original teeth has been lost, and we identify one as nonhominin. At least two adult individuals are represented. Cervix shape and the absence of common Neanderthal traits in several teeth suggest affinities with H. sapiens in both individuals, while crown and root dimensions and root morphology of all the teeth are entirely consistent with a Neanderthal attribution, pointing toward a possible shared Neanderthal and H. sapiens ancestry (the likely date of this material corresponds with the time in which both Neanderthals and H. sapiens were present in Europe). The occipital fragment is stratigraphically more recent and does not exhibit any diagnostic Neanderthal features.}, }
@article {pmid33486494, year = {2021}, author = {Kliesch, S and Schmidt, S and Wilborn, D and Aigner, C and Albrecht, W and Bedke, J and Beintker, M and Beyersdorff, D and Bokemeyer, C and Busch, J and Classen, J and de Wit, M and Dieckmann, KP and Diemer, T and Dieing, A and Gockel, M and Göckel-Beining, B and Hakenberg, OW and Heidenreich, A and Heinzelbecker, J and Herkommer, K and Hermanns, T and Kaufmann, S and Kornmann, M and Kotzerke, J and Krege, S and Kristiansen, G and Lorch, A and Müller, AC and Oechsle, K and Ohloff, T and Oing, C and Otto, U and Pfister, D and Pichler, R and Recken, H and Rick, O and Rudolph, Y and Ruf, C and Schirren, J and Schmelz, H and Schmidberger, H and Schrader, M and Schweyer, S and Seeling, S and Souchon, R and Winter, C and Wittekind, C and Zengerling, F and Zermann, DH and Zillmann, R and Albers, P}, title = {Management of Germ Cell Tumours of the Testes in Adult Patients: German Clinical Practice Guideline, PART II - Recommendations for the Treatment of Advanced, Recurrent, and Refractory Disease and Extragonadal and Sex Cord/Stromal Tumours and for the Management of Follow-Up, Toxicity, Quality of Life, Palliative Care, and Supportive Therapy.}, journal = {Urologia internationalis}, volume = {105}, number = {3-4}, pages = {181-191}, pmid = {33486494}, issn = {1423-0399}, mesh = {Adult ; Aftercare ; Humans ; Male ; Neoplasm Metastasis ; Neoplasm Recurrence, Local/therapy ; Neoplasm Staging ; Neoplasms, Germ Cell and Embryonal/pathology/*therapy ; Palliative Care ; Practice Guidelines as Topic ; Quality of Life ; Sex Cord-Gonadal Stromal Tumors/*therapy ; Testicular Neoplasms/pathology/*therapy ; }, abstract = {OBJECTIVES: We developed the first German evidence- and consensus-based clinical guideline on diagnosis, treatment, and follow-up of germ cell tumours (GCT) of the testes in adult patients. We present the guideline content in 2 separate publications. The present second part summarizes therecommendations for the treatment of advanced disease stages and for the management of follow-up and late effects.<br><br>MATERIALS AND METHODS: An interdisciplinary panel of 42 experts including 1 patient representative developed the guideline content. Clinical recommendations and statements were based on scientific evidence and expert consensus. For this purpose, evidence tables for several review questions, which were based on systematic literature searches (last search in March 2018), were provided. Thirty-one experts, who were entitled to vote, rated the final clinical recommendations and statements.<br><br>RESULTS: Here we present the treatment recommendations separately for patients with metastatic seminoma and non-seminomatous GCT (stages IIA/B and IIC/III), for restaging and treatment of residual masses, and for relapsed and refractory disease stages. The recommendations also cover extragonadal and sex cord/stromal tumours, the management of follow-up and toxicity, quality-of-life aspects, palliative care, and supportive therapy.<br><br>CONCLUSION: Physicians and other medical service providers who are involved in the diagnostics, treatment, and follow-up of GCT (all stages, outpatient and inpatient care as well as rehabilitation) are the users of the present guideline. The guideline also comprises quality indicators for measuring the implementation of the guideline recommendations in routine clinical care; these data will be presented in a future publication.}, }
@article {pmid33459351, year = {2020}, author = {VanSickle, C and Cofran, Z and Hunt, D}, title = {Did Neandertals have large brains? Factors affecting endocranial volume comparisons.}, journal = {American journal of physical anthropology}, volume = {173}, number = {4}, pages = {768-775}, doi = {10.1002/ajpa.24124}, pmid = {33459351}, issn = {1096-8644}, mesh = {Adult ; Aged ; Aged, 80 and over ; Animals ; Anthropology, Physical ; Brain/*anatomy &amp; histology ; Cephalometry ; Female ; Fossils ; Humans ; Male ; Middle Aged ; Neanderthals/*anatomy &amp; histology ; Sex Characteristics ; Skull/*anatomy &amp; histology ; Young Adult ; }, abstract = {OBJECTIVES: Common wisdom in paleoanthropology is that Neandertals had bigger brains than recent humans. Here we tested the hypothesis that there is no difference in brain size between Neandertals and recent humans while accounting for methodological variation and the makeup of both the Neandertal and recent human samples.<br><br>MATERIALS AND METHODS: We examined endocranial volume (ECV) derived from virtually reconstructed endocasts of 11 Neandertals, six of which had associated femoral head diameters (FHD). Our recent human comparative dataset consisted of virtually measured ECV and associated FHD from 94 recent humans from the Robert J. Terry Anatomical Collection (63 male, 31 female). ECV of Neandertals and recent humans was compared using bootstrap resampling, repeating the analysis for two groupings of Neandertals (all and classic) and for three groupings of recent humans (all, males, and females). To examine brain size scaling, we completed an ordinary least squares regression of log (ECV) against log (FHD) for Neandertals and recent humans.<br><br>RESULTS: The results of the bootstrap resampling analyses indicated that Neandertals only had significantly larger ECV when compared with recent human females. The regression between ECV and FHD suggested that Neandertals fall within the range of variation for larger humans.<br><br>DISCUSSION: Our results demonstrate that Neandertals do not have uniquely large brains when compared with recent humans. Their brain size falls in the large end of the recent human range of variation, but does not exceed it. These results have implications for future research on Neandertal encephalization.}, }
@article {pmid33454959, year = {2021}, author = {Towle, I and Loch, C}, title = {Tooth chipping prevalence and patterns in extant primates.}, journal = {American journal of physical anthropology}, volume = {175}, number = {1}, pages = {292-299}, doi = {10.1002/ajpa.24232}, pmid = {33454959}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Dental Enamel/pathology ; *Diet ; Fossils ; Prevalence ; Primates/*anatomy &amp; histology ; Tooth/*pathology ; *Tooth Fractures/epidemiology/pathology/veterinary ; }, abstract = {OBJECTIVES: A tooth chip occurs when a hard object forcefully contacts the surface of the tooth, typically removing enamel from the occlusal edge. In this study, chipping patterns in extant primates were compared, and hard-object-feeding assessed alongside other factors (e.g., grit mastication and dental properties), to elucidate dietary and behavioral inferences in archeological and paleontological samples.<br><br>MATERIALS AND METHODS: Thirteen species of extant primates were studied, including eight species within the Cercopithecidae, two within the Ceboidea, and three within the Hominoidea. Four additional species were also incorporated from the literature for some of the analyses. The severity (Grade 1-3), position (buccal, lingual, mesial, and distal) and number of tooth fractures were recorded for each specimen.<br><br>RESULTS: Species considered hard-object-feeding specialists presented higher rates of chipping, with sakis, mandrills, sooty mangabeys and Raffles' banded langurs having high chipping rates (28.3%, 36.7%, 48.4%, and 34.7% of teeth, respectively). Species that seasonally eat harder foods had intermediate chipping frequencies (e.g., brown woolly monkeys: 18.5%), and those that less commonly consume hard food items had the lowest chipping frequencies (e.g., Kloss gibbon: 7.3%; chimpanzees: 4.4%).<br><br>DISCUSSION: The results suggest hard food mastication influences differences in chipping prevalence among the species studied. Although Homo fossil samples show high rates of chipping comparable to hard-object-feeding extant primates, they display a different pattern of chipping, supporting the hypothesis that these fractures are mostly non-food related (e.g., grit mastication in Homo naledi; non-masticatory tooth use in Neanderthals).}, }
@article {pmid33446842, year = {2021}, author = {Pederzani, S and Aldeias, V and Dibble, HL and Goldberg, P and Hublin, JJ and Madelaine, S and McPherron, SP and Sandgathe, D and Steele, TE and Turq, A and Britton, K}, title = {Reconstructing Late Pleistocene paleoclimate at the scale of human behavior: an example from the Neandertal occupation of La Ferrassie (France).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1419}, pmid = {33446842}, issn = {2045-2322}, mesh = {Animals ; *Archaeology ; *Behavior, Animal ; *Fossils ; France ; Humans ; *Neanderthals ; }, abstract = {Exploring the role of changing climates in human evolution is currently impeded by a scarcity of climatic information at the same temporal scale as the human behaviors documented in archaeological sites. This is mainly caused by high uncertainties in the chronometric dates used to correlate long-term climatic records with archaeological deposits. One solution is to generate climatic data directly from archaeological materials representing human behavior. Here we use oxygen isotope measurements of Bos/Bison tooth enamel to reconstruct summer and winter temperatures in the Late Pleistocene when Neandertals were using the site of La Ferrassie. Our results indicate that, despite the generally cold conditions of the broader period and despite direct evidence for cold features in certain sediments at the site, Neandertals used the site predominantly when climatic conditions were mild, similar to conditions in modern day France. We suggest that due to millennial scale climate variability, the periods of human activity and their climatic characteristics may not be representative of average conditions inferred from chronological correlations with long-term climatic records. These results highlight the importance of using direct routes, such as the high-resolution archives in tooth enamel from anthropogenically accumulated faunal assemblages, to establish climatic conditions at a human scale.}, }
@article {pmid33441416, year = {2021}, author = {Dumas, G and Malesys, S and Bourgeron, T}, title = {Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition.}, journal = {Genome research}, volume = {31}, number = {3}, pages = {484-496}, pmid = {33441416}, issn = {1549-5469}, mesh = {Animals ; Brain/*metabolism ; Brain Diseases/genetics ; *Cognition ; DNA Damage/genetics ; DNA Repair Enzymes/genetics ; *Evolution, Molecular ; Humans ; Primates/*genetics ; Proteins/*genetics ; Selection, Genetic ; }, abstract = {The human brain differs from that of other primates, but the genetic basis of these differences remains unclear. We investigated the evolutionary pressures acting on almost all human protein-coding genes (N = 11,667; 1:1 orthologs in primates) based on their divergence from those of early hominins, such as Neanderthals, and non-human primates. We confirm that genes encoding brain-related proteins are among the most strongly conserved protein-coding genes in the human genome. Combining our evolutionary pressure metrics for the protein-coding genome with recent data sets, we found that this conservation applied to genes functionally associated with the synapse and expressed in brain structures such as the prefrontal cortex and the cerebellum. Conversely, several genes presenting signatures commonly associated with positive selection appear as causing brain diseases or conditions, such as micro/macrocephaly, Joubert syndrome, dyslexia, and autism. Among those, a number of DNA damage response genes associated with microcephaly in humans such as BRCA1, NHEJ1, TOP3A, and RNF168 show strong signs of positive selection and might have played a role in human brain size expansion during primate evolution. We also showed that cerebellum granule neurons express a set of genes also presenting signatures of positive selection and that may have contributed to the emergence of fine motor skills and social cognition in humans. This resource is available online and can be used to estimate evolutionary constraints acting on a set of genes and to explore their relative contributions to human traits.}, }
@article {pmid33436796, year = {2021}, author = {McGrath, K and Limmer, LS and Lockey, AL and Guatelli-Steinberg, D and Reid, DJ and Witzel, C and Bocaege, E and McFarlin, SC and El Zaatari, S}, title = {3D enamel profilometry reveals faster growth but similar stress severity in Neanderthal versus Homo sapiens teeth.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {522}, pmid = {33436796}, issn = {2045-2322}, mesh = {*Adverse Childhood Experiences ; Animals ; Child ; Dental Enamel/diagnostic imaging/*growth &amp; development/*pathology ; Hominidae/*anatomy &amp; histology ; Humans ; Imaging, Three-Dimensional/*methods ; Moire Topography/*methods ; Neanderthals/*anatomy &amp; histology ; Species Specificity ; Tooth/diagnostic imaging/*growth &amp; development/pathology ; }, abstract = {Early life stress disrupts growth and creates horizontal grooves on the tooth surface in humans and other mammals, yet there is no consensus for their quantitative analysis. Linear defects are considered to be nonspecific stress indicators, but evidence suggests that intermittent, severe stressors create deeper defects than chronic, low-level stressors. However, species-specific growth patterns also influence defect morphology, with faster-growing teeth having shallower defects at the population level. Here we describe a method to measure the depth of linear enamel defects and normal growth increments (i.e., perikymata) from high-resolution 3D topographies using confocal profilometry and apply it to a diverse sample of Homo neanderthalensis and H. sapiens anterior teeth. Debate surrounds whether Neanderthals exhibited modern human-like growth patterns in their teeth and other systems, with some researchers suggesting that they experienced more severe childhood stress. Our results suggest that Neanderthals have shallower features than H. sapiens from the Upper Paleolithic, Neolithic, and medieval eras, mirroring the faster growth rates in Neanderthal anterior teeth. However, when defect depth is scaled by perikymata depth to assess their severity, Neolithic humans have less severe defects, while Neanderthals and the other H. sapiens groups show evidence of more severe early life growth disruptions.}, }
@article {pmid33429259, year = {2021}, author = {Heydari, M and Guérin, G and Zeidi, M and Conard, NJ}, title = {Bayesian luminescence dating at Ghār-e Boof, Iran, provides a new chronology for Middle and Upper Paleolithic in the southern Zagros.}, journal = {Journal of human evolution}, volume = {151}, number = {}, pages = {102926}, doi = {10.1016/j.jhevol.2020.102926}, pmid = {33429259}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; Bayes Theorem ; Caves ; Humans ; Iran ; Luminescence ; *Neanderthals ; *Radiometric Dating ; }, abstract = {Ghār-e Boof is a Paleolithic cave site in Iran well known for its rich early Upper Paleolithic Rostamian assemblages. The site is located on the edge of the Dasht-e Rostam plain in the southern Zagros. Recent excavations by the members of the Tübingen-Iranian Stone Age Research Project at Ghār-e Boof also recovered well-stratified Middle Paleolithic assemblages. Here, we provide the first detailed luminescence chronology for the Middle and Upper Paleolithic of the site. More generally, our work is the first luminescence chronology for a Middle and Upper Paleolithic site in the Zagros Mountains region in Iran. The luminescence ages for the Upper Paleolithic of Ghār-e Boof agree with published [14]C dates. We applied Bayesian models specifically designed for luminescence dating using the R package 'BayLum' to incorporate the well-established stratigraphic constraints, as well as the published [14]C ages with our optically stimulated luminescence (OSL) ages to improve the precision of the chronological framework. The Bayesian chronology shows a significantly improved precision of the OSL ages in particular for the upper part of the sequence where [14]C ages were available. The Bayesian OSL ages for the Rostamian horizons, archaeologicalhorizon (AH) III (a-b-c), and AH IV, fall in the range of 37-42 ka (68% credible interval [CI]). Moreover, we determined a series of dates between 45 and 81 ka (68% CI) for the Middle Paleolithic strata from AH IVd to AH VI. Our results point to a demographic shift in the populations responsible for the Middle Paleolithic and the Rostamian within three millennia. This major technological change accompanied by the rise of symbolic artifacts such as personal ornaments, may or may not reflect a replacement of Neanderthals by modern humans. While we are confident that the Rostamian was made by modern humans, available information does not allow us to be sure who made the local Middle Paleolithic.}, }
@article {pmid33418451, year = {2021}, author = {Nowaczewska, W and Binkowski, M and Benazzi, S and Vazzana, A and Nadachowski, A and Stefaniak, K and Żarski, M and Talamo, S and Compton, T and Stringer, CB and Hajdinjak, M and Hublin, JJ}, title = {New hominin teeth from Stajnia Cave, Poland.}, journal = {Journal of human evolution}, volume = {151}, number = {}, pages = {102929}, doi = {10.1016/j.jhevol.2020.102929}, pmid = {33418451}, issn = {1095-8606}, mesh = {Animals ; Caves ; Fossils/*anatomy &amp; histology ; Hominidae/*anatomy &amp; histology ; Paleodontology ; Poland ; Tooth/*anatomy &amp; histology ; }, }
@article {pmid33417716, year = {2021}, author = {Greer, C and Bhakta, H and Ghanem, L and Refai, F and Linn, E and Avella, M}, title = {Deleterious variants in genes regulating mammalian reproduction in Neanderthals, Denisovans and extant humans.}, journal = {Human reproduction (Oxford, England)}, volume = {36}, number = {3}, pages = {734-755}, doi = {10.1093/humrep/deaa347}, pmid = {33417716}, issn = {1460-2350}, mesh = {Animals ; Europe ; Genome, Human ; *Hominidae/genetics ; Humans ; Male ; *Neanderthals/genetics ; Nuclear Proteins ; Reproduction/genetics ; Trans-Activators ; }, abstract = {STUDY QUESTION: Were Neanderthals and Denisovans (referred here also as extinct hominidae) carrying deleterious variants in genes regulating reproduction?<br><br>SUMMARY ANSWER: The majority of extinct hominidae analyzed here, presented a considerable number of deleterious variants per individual in proteins regulating different aspects of reproduction, including gonad and uterine function, and gametogenesis.<br><br>WHAT IS KNOWN ALREADY: Neanderthals, Denisovans and extant humans were interfertile and hybridized while occupying geographically overlapping areas in Europe and Asia. This is evidenced by the small archaic genome component (average &#x223c;2%) present in non-African extant humans.<br><br>STUDY DESIGN, SIZE, DURATION: The genome of eight extinct hominidae, together with five human genome databases, plus 44 mothers and 48 fathers (fertile controls), were screened to look for deleterious variants in 1734 protein-coding genes regulating reproduction.<br><br>Ancient DNA from six Neanderthals and two Denisovans dated between &#x223c;82&#xa0;000 and 43&#xa0;000 calibrated years was retrieved from the public European Nucleotide Archive. The hominins analyzed include Altai, Vindija 33.15, 33.19, 33.25 and 33.26, El Sidron 1253, Denisova 3 and 11. Their DNA was analyzed using the CLC Genomics Workbench 12, by mapping overlapping paired-end reads (Illumina, FASTQ files) to the human genome assembly GRCh37 (hg19) (Vindija 33.19, 33.25, 33.26, Denisova 3 and Denisova 11) or by analyzing BAM files (Altai, El Sidron 1253 and Vindija 33.15) (human genome reference, GRCh37 (hg19)). Non-synonymous reproductive variants were classified as deleterious or tolerated (PolyPhen-2 and SIFT analyses) and were compared to deleterious variants obtained from extant human genome databases (Genome Aggregation Database (GnomAD), 1000 Genomes, the Haplotype Map (HapMap), Single Nucleotide Polymorphism Database (dbSNPs)) across different populations. A genetic intersection between extant or extinct DNA variants and other genetic disorders was evaluated by annotating the obtained variants with the Clinical Variant (ClinVar) database.<br><br>Among the eight extinct hominidae analyzed, a total of 9650 non-synonymous variants (only coverage &#x2265;20 reads included; frameshift mutations were excluded) in 1734 reproductive protein-coding genes were found, 24% of which were classified as deleterious. The majority (73%) of the deleterious alleles present in extant humans that are shared between extant humans and extinct hominidae were found to be rare (<1%) in extant human populations. A set of 8044 variants were found uniquely in extinct hominidae. At the single-gene level, no extinct individual was found to be homozygous for deleterious variants in genes necessary for gamete recognition and fusion, and no higher chance of embryo-lethality (calculated by Mendelian Genetics) was found upon simulated mating between extant human and extinct hominidae compared to extant human-extant human. However, three of the eight extinct hominidae were found to be homozygous for 48-69 deleterious variants in 55 genes controlling ovarian and uterine functions, or oogenesis (AKAP1, BUB1B, CCDC141, CDC73, DUSP6, ESR1, ESR2, PATL2, PSMC3IP, SEMA3A, WT1 and WNT4). Moreover, we report the distribution of nine Neanderthal variants in genes associated with a human fertility phenotype found in extant human populations, one of which has been associated with polycystic ovarian syndrome and primary congenital glaucoma.<br><br>While analyzing archaic DNA, stringent filtering criteria were adopted to screen for deleterious variants in Neanderthals and Denisovans, which could result in missing a number of variants. Such restraints preserve the potential for detection of additional deleterious variants in reproductive proteins in extinct hominidae.<br><br>This study provides a comprehensive overview of putatively deleterious variants in extant human populations and extinct individuals occurring in 1734 protein-coding genes controlling reproduction and provides the fundaments for future functional studies of extinct variants in human reproduction.<br><br>This study was supported by the Department of Biological Science and by the Office of Research and Sponsored Programs at the University of Tulsa (Faculty Research Grant and Faculty Research Summer Fellowship) to M.A. and the University of Tulsa, Tulsa Undergraduate Research Challenge (TURC) program to E.L.; no conflict of interest to declare.<br><br>TRIAL REGISTRATION NUMBER: N/A.}, }
@article {pmid33412555, year = {2021}, author = {Kliesch, S and Schmidt, S and Wilborn, D and Aigner, C and Albrecht, W and Bedke, J and Beintker, M and Beyersdorff, D and Bokemeyer, C and Busch, J and Classen, J and de Wit, M and Dieckmann, KP and Diemer, T and Dieing, A and Gockel, M and Göckel-Beining, B and Hakenberg, OW and Heidenreich, A and Heinzelbecker, J and Herkommer, K and Hermanns, T and Kaufmann, S and Kornmann, M and Kotzerke, J and Krege, S and Kristiansen, G and Lorch, A and Müller, AC and Oechsle, K and Ohloff, T and Oing, C and Otto, U and Pfister, D and Pichler, R and Recken, H and Rick, O and Rudolph, Y and Ruf, C and Schirren, J and Schmelz, H and Schmidberger, H and Schrader, M and Schweyer, S and Seeling, S and Souchon, R and Winter, C and Wittekind, C and Zengerling, F and Zermann, DH and Zillmann, R and Albers, P}, title = {Management of Germ Cell Tumours of the Testis in Adult Patients. German Clinical Practice Guideline Part I: Epidemiology, Classification, Diagnosis, Prognosis, Fertility Preservation, and Treatment Recommendations for Localized Stages.}, journal = {Urologia internationalis}, volume = {105}, number = {3-4}, pages = {169-180}, pmid = {33412555}, issn = {1423-0399}, mesh = {Adult ; Fertility Preservation ; Humans ; Male ; Neoplasm Staging ; *Neoplasms, Germ Cell and Embryonal/classification/diagnosis/epidemiology/therapy ; Practice Guidelines as Topic ; Prognosis ; *Testicular Neoplasms/classification/diagnosis/epidemiology/therapy ; }, abstract = {INTRODUCTION: This is the first German evidence- and consensus-based clinical guideline on diagnosis, treatment, and follow-up on germ cell tumours (GCTs) of the testis in adult patients. We present the guideline content in two publications. Part I covers the topic's background, methods, epidemiology, classification systems, diagnostics, prognosis, and treatment recommendations for the localized stages.<br><br>METHODS: An interdisciplinary panel of 42 experts including 1 patient representative developed the guideline content. Clinical recommendations and statements were based on scientific evidence and expert consensus. For this purpose, evidence tables for several review questions, which were based on systematic literature searches (last search was in March 2018) were provided. Thirty-one experts entitled to vote, rated the final clinical recommendations and statements.<br><br>RESULTS: We provide 161 clinical recommendations and statements. We present information on the quality of cancer care and epidemiology and give recommendations for staging and classification as well as for diagnostic procedures. The diagnostic recommendations encompass measures for assessing the primary tumour as well as procedures for the detection of metastases. One chapter addresses prognostic factors. In part I, we separately present the treatment recommendations for germ cell neoplasia in situ, and the organ-confined stages (clinical stage I) of both seminoma and nonseminoma.<br><br>CONCLUSION: Although GCT is a rare tumour entity with excellent survival rates for the localized stages, its management requires an interdisciplinary approach, including several clinical experts. Quality of care is highly related to institutional expertise and can be reassured by established online-based second-opinion boards. There are very few studies on diagnostics with good level of evidence. Treatment of metastatic GCTs must be tailored to the risk according to the International Germ Cell Cancer Collaboration Group classification after careful diagnostic evaluation. An interdisciplinary approach as well as the referral of selected patients to centres with proven experience can help achieve favourable clinical outcomes.}, }
@article {pmid33412453, year = {2021}, author = {Dodat, PJ and Tacail, T and Albalat, E and Gómez-Olivencia, A and Couture-Veschambre, C and Holliday, T and Madelaine, S and Martin, JE and Rmoutilova, R and Maureille, B and Balter, V}, title = {Isotopic calcium biogeochemistry of MIS 5 fossil vertebrate bones: application to the study of the dietary reconstruction of Regourdou 1 Neandertal fossil.}, journal = {Journal of human evolution}, volume = {151}, number = {}, pages = {102925}, doi = {10.1016/j.jhevol.2020.102925}, pmid = {33412453}, issn = {1095-8606}, mesh = {Animals ; Bone and Bones/*chemistry ; Calcium Isotopes/*analysis ; *Diet ; *Fossils ; France ; *Neanderthals ; *Vertebrates ; }, abstract = {The calcium isotopic composition (δ[44/42]Ca) of bone and tooth enamel can be used for dietary reconstructions of extant and extinct mammals. In natural conditions, the δ[44/42]Ca value of bone and teeth varies according to dietary intake with a constant isotopic offset of about -0.6‰. Owing to the poor conservation of collagen, carbon (C), and nitrogen (N) isotopic compositions of the Regourdou Mousterian site (MIS 5, Dordogne, France) previously failed to provide any paleodietary information. Therefore, to reconstruct the trophic chain, we have measured calcium (Ca) isotopes from fossil bone samples of the fauna from the Regourdou site, as well as from three bone samples of the Regourdou 1 Neandertal specimen. The results show a taxon-dependent patterning of the Ca isotopic compositions: herbivores generally have higher δ[44/42]Ca values than carnivores. All the δ[44/42]Ca values of Regourdou 1 are low (<-1.6‰), placing this specimen amid carnivores. Using a bone-muscle Ca isotopic offset determined on extant animals, we further show that the δ[44/42]Ca value of the Regourdou 1 diet, and that of most carnivores, cannot be accounted for by the consumption of meat only, as plants and meat have indistinguishable δ[44/42]Ca values. Mass balance calculations indicate that the low δ[44/42]Ca values of the Neandertal's carnivorous diet are explained by the ingestion of bone marrow containing as little as 1% trabecular bone. Our results show that the Regourdou 1 Neanderthal consumed a mixture of various herbivorous prey, as well as trabecular bone, which probably occurred when marrow was ingested, by accident or intentionally.}, }
@article {pmid33370643, year = {2021}, author = {Cullen, VL and Smith, VC and Tushabramishvili, N and Mallol, C and Dee, M and Wilkinson, KN and Adler, DS}, title = {A revised AMS and tephra chronology for the Late Middle to Early Upper Paleolithic occupations of Ortvale Klde, Republic of Georgia.}, journal = {Journal of human evolution}, volume = {151}, number = {}, pages = {102908}, doi = {10.1016/j.jhevol.2020.102908}, pmid = {33370643}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; *Caves ; Fossils ; Georgia (Republic) ; *Hominidae ; Humans ; Neanderthals ; *Radiometric Dating ; Volcanic Eruptions/analysis ; }, abstract = {The nature and timing of the shift from the Late Middle Paleolithic (LMP) to the Early Upper Paleolithic (EUP) varied geographically, temporally, and substantively across the Near East and Eurasia; however, the result of this process was the archaeological disappearance of Middle Paleolithic technologies across the length and breadth of their geographic distribution. Ortvale Klde rockshelter (Republic of Georgia) contains the most detailed LMP-EUP archaeological sequence in the Caucasus, an environmentally and topographically diverse region situated between southwest Asia and Europe. Tephrochronological investigations at the site reveal volcanic ash (tephra) from various volcanic sources and provide a tephrostratigraphy for the site that will facilitate future correlations in the region. We correlate one of the cryptotephra layers to the large, caldera-forming Nemrut Formation eruption (30,000 years ago) from Nemrut volcano in Turkey. We integrate this tephrochronological constraint with new radiocarbon dates and published ages in an OxCal Bayesian age model to produce a revised chronology for the site. This model increases the ages for the end of the LMP (∼47.5-44.2 ka cal BP) and appearance of the EUP (∼46.7-43.6 ka cal BP) at Ortvale Klde, which are earlier than those currently reported for other sites in the Caucasus but similar to estimates for specific sites in southwest Asia and eastern Europe. These data, coupled with archaeological, stratigraphic, and taphonomic observations, suggest that at Ortvale Klde, (1) the appearance of EUP technologies of bone and stone has no technological roots in the preceding LMP, (2) a LMP population vacuum likely preceded the appearance of these EUP technologies, and (3) the systematic combination of tephra correlations and absolute dating chronologies promises to substantially improve our inter-regional understanding of this critical time interval of human evolution and the potential interconnectedness of hominins at different sites.}, }
@article {pmid33362257, year = {2020}, author = {González-Molina, I and Jiménez-García, B and Maíllo-Fernández, JM and Baquedano, E and Domínguez-Rodrigo, M}, title = {Distinguishing Discoid and Centripetal Levallois methods through machine learning.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0244288}, pmid = {33362257}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Archaeology/*methods ; Fossils/*diagnostic imaging ; Hominidae ; Humans ; Inventions ; Machine Learning ; Neanderthals ; Technology ; Tool Use Behavior/*classification ; }, abstract = {In this paper, we apply Machine Learning (ML) algorithms to study the differences between Discoid and Centripetal Levallois methods. For this purpose, we have used experimentally knapped flint flakes, measuring several parameters that have been analyzed by seven ML algorithms. From these analyses, it has been possible to demonstrate the existence of statistically significant differences between Discoid products and Centripetal Levallois products, thus contributing with new data and a new method to this traditional debate. The new approach enabled differentiating the blanks created by both knapping methods with an accuracy >80% using only ten typometric variables. The most relevant variables were maximum length, width to the 25%, 50% and 75% of the flake length, external and internal platform angles, maximum width and number of dorsal scars. This study also demonstrates the advantages of the application of multivariate ML methods to lithic studies.}, }
@article {pmid33360685, year = {2021}, author = {Adegboyega, MT and Stamos, PA and Hublin, JJ and Weaver, TD}, title = {Virtual reconstruction of the Kebara 2 Neanderthal pelvis.}, journal = {Journal of human evolution}, volume = {151}, number = {}, pages = {102922}, doi = {10.1016/j.jhevol.2020.102922}, pmid = {33360685}, issn = {1095-8606}, mesh = {Animals ; Fossils/*anatomy &amp; histology ; Male ; Neanderthals/*anatomy &amp; histology ; Observer Variation ; Pelvis/*anatomy &amp; histology ; Printing, Three-Dimensional ; Tomography, X-Ray Computed ; }, abstract = {The paucity of well-preserved pelvises in the hominin fossil record has hindered robust analyses of shifts in critical biological processes throughout human evolution. The Kebara 2 pelvis remains one of the best preserved hominin pelvises, providing a rare opportunity to assess Neanderthal pelvic morphology and function. Here, we present two new reconstructions of the Kebara 2 pelvis created from CT scans of the right hip bone and sacrum. For both reconstructions, we proceeded as follows. First, we virtually reconstructed the right hip bone and the sacrum by repositioning the fragments of the hip bone and sacrum. Then, we created a mirrored copy of the right hip bone to act as the left hip bone. Next, we 3D printed the three bones and physically articulated them. Finally, we used fiducial points collected from the physically articulated models to articulate the hip bones and sacrum in virtual space. Our objectives were to (1) reposition misaligned fragments, particularly the ischiopubic ramus; (2) create a 3D model of a complete pelvis; and (3) assess interobserver reconstruction variation. These new reconstructions show that, in comparison with previous measurements, Kebara 2 possessed a higher shape index (maximum anteroposterior length/maximum mediolateral width) for the pelvic inlet and perhaps the outlet and a more anteriorly positioned sacral promontory and pubic symphysis relative to the acetabula. The latter differences result in a lower ratio between the distances anterior and posterior to the anterior margins of the acetabula. Generally, the new reconstructions tend to accentuate features of the Kebara 2 pelvis--the long superior pubic ramus and anteriorly positioned pelvic inlet--that have already been discussed for Kebara 2 and other Neanderthals.}, }
@article {pmid33356949, year = {2021}, author = {Higgitt, R}, title = {Neanderthal and the fossilization of the Third World.}, journal = {Social studies of science}, volume = {51}, number = {3}, pages = {439-462}, doi = {10.1177/0306312720983460}, pmid = {33356949}, issn = {1460-3659}, mesh = {Animals ; Europe ; Humans ; *Neanderthals ; Whites ; }, abstract = {Neanderthal is the quintessential scientific Other. In the late nineteenth century gentlemen-scientists, including business magnates, investment bankers and lawmakers with interest in questions of human and human societal development, framed Europe's Neanderthal and South Asia's indigenous Negritos as close evolutionary kin. Simultaneously, they explained Neanderthal's extinction as the consequence of an inherent backwardness in the face of fair-skinned, steadily-progressing newcomers to ancient Europe who behaved in ways associated with capitalism. This racialization and economization of Neanderthal helped bring meaning and actual legal reality to Negritos via the British Raj's official 'schedules of backward castes and tribes'. It also helped justify the Raj's initiation of market-oriented reforms in order to break a developmental equilibrium deemed created when fair-skinned newcomers to ancient South Asia enslaved Negritos in an enduring caste system. Neanderthal was integral to the scientism behind the British construction of caste, and contributed to India's becoming a principal 'Third World' target of Western structural adjustment policies as continuation of South Asia's 'evolution assistance'.}, }
@article {pmid33351193, year = {2021}, author = {Reichheld, SE and Muiznieks, LD and Huynh, Q and Wang, N and Ing, C and Miao, M and Sitarz, EE and Pomès, R and Sharpe, S and Keeley, FW}, title = {The evolutionary background and functional consequences of the rs2071307 polymorphism in human tropoelastin.}, journal = {Biopolymers}, volume = {112}, number = {2}, pages = {e23414}, doi = {10.1002/bip.23414}, pmid = {33351193}, issn = {1097-0282}, support = {FRN399475/CAPMC/CIHR/Canada ; FRN399475/CAPMC/CIHR/Canada ; }, mesh = {Animals ; Evolution, Molecular ; Gene Frequency ; Humans ; Hydrophobic and Hydrophilic Interactions ; Molecular Dynamics Simulation ; Neanderthals/genetics ; Nuclear Magnetic Resonance, Biomolecular ; *Polymorphism, Single Nucleotide ; Tropoelastin/*chemistry/*genetics/metabolism ; }, abstract = {Elastin is a major polymeric protein of the extracellular matrix, providing critical properties of extensibility and elastic recoil. The rs2071307 genomic polymorphism, resulting in the substitution of a serine for a glycine residue in a VPG motif in tropoelastin, has an unusually high minor allele frequency in humans. A consequence of such allelic heterozygosity would be the presence of a heterogeneous elastin polymer in up to 50% of the population, a situation which appears to be unique to Homo sapiens. VPG motifs are extremely common in hydrophobic domains of tropoelastins and are the sites of transient β-turns that are essential for maintaining the conformational flexibility required for its function as an entropic elastomer. Earlier data demonstrated that single amino acid substitutions in tropoelastin can have functional consequences for polymeric elastin, particularly when present in mixed polymers. Here, using NMR and molecular dynamics approaches, we show the rs2071307 polymorphism reduces local propensity for β-turn formation, with a consequent increase in polypeptide hydration and an expansion of the conformational ensemble manifested as an increased hydrodynamic radius, radius of gyration and asphericity. Furthermore, this substitution affects functional properties of polymeric elastin, particularly in heterogeneous polymers mimicking allelic heterozygosity. We discuss whether such effects, together with the unusually high minor allele frequency of the polymorphism, could imply some some evolutionary advantage for the heterozygous state.}, }
@article {pmid33343925, year = {2020}, author = {Kist, NC and Lambert, B and Campbell, S and Katzourakis, A and Lunn, D and Lemey, P and Iversen, AKN}, title = {HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification.}, journal = {Virus evolution}, volume = {6}, number = {2}, pages = {veaa085}, pmid = {33343925}, issn = {2057-1577}, abstract = {Pathogen-driven selection and past interbreeding with archaic human lineages have resulted in differences in human leukocyte antigen (HLA)-allele frequencies between modern human populations. Whether or not this variation affects pathogen subtype diversification is unknown. Here we show a strong positive correlation between ethnic diversity in African countries and both human immunodeficiency virus (HIV)-1 p24gag and subtype diversity. We demonstrate that ethnic HLA-allele differences between populations have influenced HIV-1 subtype diversification as the virus adapted to escape common antiviral immune responses. The evolution of HIV Subtype B (HIV-B), which does not appear to be indigenous to Africa, is strongly affected by immune responses associated with Eurasian HLA variants acquired through adaptive introgression from Neanderthals and Denisovans. Furthermore, we show that the increasing and disproportionate number of HIV-infections among African Americans in the USA drive HIV-B evolution towards an Africa-centric HIV-1 state. Similar adaptation of other pathogens to HLA variants common in affected populations is likely.}, }
@article {pmid33341120, year = {2020}, author = {Árnason, &#xda; and Hallström, B}, title = {The reversal of human phylogeny: Homo left Africa as erectus, came back as sapiens sapiens.}, journal = {Hereditas}, volume = {157}, number = {1}, pages = {51}, pmid = {33341120}, issn = {1601-5223}, mesh = {Africa ; Animals ; *Biological Evolution ; Cytogenetic Analysis ; DNA, Mitochondrial ; Environment ; Evolution, Molecular ; Gene-Environment Interaction ; *Genetics, Population ; Hominidae/*classification/*genetics ; *Human Genetics ; Humans ; *Phylogeny ; }, abstract = {BACKGROUND: The molecular out of Africa hypothesis, OOAH, has been considered as an established fact amid population geneticists for some 25-30 years despite the early concern with it among phylogeneticists with experience beyond that of Homo. The palaeontological support for the hypothesis is also questionable, a circumstance that in the light of expanding Eurasian palaeontological knowledge has become accentuated through the last decades.<br><br>RESULTS: The direction of evolution in the phylogenetic tree of modern humans (Homo sapiens sapiens, Hss) was established inter alia by applying progressive phylogenetic analysis to an mtDNA sampling that included a Eurasian, Lund, and the African Mbuti, San and Yoruba. The examination identified the African populations as paraphyletic, thereby compromising the OOAH. The finding, which was consistent with the out of Eurasia hypothesis, OOEH, was corroborated by the mtDNA introgression from Hss into Hsnn (Neanderthals) that demonstrated the temporal and physical Eurasian coexistence of the two lineages. The results are consistent with the palaeontologically established presence of H. erectus in Eurasia, a Eurasian divergence between H. sapiens and H. antecessor &#x2248; 850,000 YBP, an Hs divergence between Hss and Hsn (Neanderthals + Denisovans)&#x2009;&#x2248;&#x2009;800,000 YBP, an mtDNA introgression from Hss into Hsnn*&#xa0;&#x2248;&#x2009;500,000 YBP and an Eurasian divergence among the ancestors of extant Hss &#x2248; 250,000 YBP at the exodus of Mbuti/San into Africa.<br><br>CONCLUSIONS: The present study showed that Eurasia was not the receiver but the donor in Hss evolution. The findings that Homo left Africa as erectus and returned as sapiens sapiens constitute a change in the understanding of Hs evolution to one that conforms to the extensive Eurasian record of Hs palaeontology and archaeology.}, }
@article {pmid33339234, year = {2020}, author = {Vizzari, MT and Benazzo, A and Barbujani, G and Ghirotto, S}, title = {A Revised Model of Anatomically Modern Human Expansions Out of Africa through a Machine Learning Approximate Bayesian Computation Approach.}, journal = {Genes}, volume = {11}, number = {12}, pages = {}, pmid = {33339234}, issn = {2073-4425}, mesh = {Africa ; Animals ; Asia ; Bayes Theorem ; Biological Evolution ; *Computer Simulation ; Europe ; Genetic Variation ; *Genome, Human ; History, Ancient ; *Hominidae ; Human Migration/*history ; Humans ; *Machine Learning ; *Models, Theoretical ; Neanderthals/genetics ; Racial Groups/genetics ; }, abstract = {There is a wide consensus in considering Africa as the birthplace of anatomically modern humans (AMH), but the dispersal pattern and the main routes followed by our ancestors to colonize the world are still matters of debate. It is still an open question whether AMH left Africa through a single process, dispersing almost simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Australo-Melanesia, and later through a northern route crossing the Levant. The development of new methodologies for inferring population history and the availability of worldwide high-coverage whole-genome sequences did not resolve this debate. In this work, we test the two main out-of-Africa hypotheses through an Approximate Bayesian Computation approach, based on the Random-Forest algorithm. We evaluated the ability of the method to discriminate between the alternative models of AMH out-of-Africa, using simulated data. Once assessed that the models are distinguishable, we compared simulated data with real genomic variation, from modern and archaic populations. This analysis showed that a model of multiple dispersals is four-fold as likely as the alternative single-dispersal model. According to our estimates, the two dispersal processes may be placed, respectively, around 74,000 and around 46,000 years ago.}, }
@article {pmid33301927, year = {2021}, author = {Jaimes Díaz, H and Martínez Covarrubias, EI and Murcia Garzón, JE and Flores Valdez, M and Muñoz Ramírez, ZY and Ramírez Calzada, CA and Bohra, R and Méndez Tenorio, A}, title = {Phylogenomic study and classification of mitochondrial DNA through virtual genomic fingerprints.}, journal = {Mitochondrion}, volume = {57}, number = {}, pages = {294-299}, doi = {10.1016/j.mito.2020.11.016}, pmid = {33301927}, issn = {1872-8278}, mesh = {Animals ; Computer Simulation ; DNA Fingerprinting/*methods ; DNA, Mitochondrial/classification/*genetics ; Genomics/*methods ; Haplotypes ; Humans ; Mitochondria/*classification/genetics ; Neanderthals/genetics ; Pan paniscus/genetics ; Pan troglodytes/genetics ; Phylogeny ; }, abstract = {In the present study, we evaluated the ability of the Virtual Analysis Method for Phylogenomic fingerprint Estimation (VAMPhyRE) toolkit to classify human mitochondrial DNA (mtDNA) haplogroups. In total, 357 random mtDNA sequences were obtained from different haplogroups, based on the classification of PhyloTree. Additionally, we included a control group of five sequences (Pan paniscus, Pan troglodytes, Homo sapiens neanderthalensis, Yoruba15, and the revised Cambridge reference sequence). VAMPhyRE employs a virtual hybridization technique, using probes that specifically bind to their complementary sequences in the genome. We used 65,536 probes of 8 nucleotides to identify potential sites where hybridization occurs between the mtDNA and the specific probe, forming different heteroduplexes and thus, creating a unique and specific genomic fingerprint for each sequence. Genomic fingerprints were compared, and a table of distances was calculated to obtain a mitochondrial phylogenomic tree with the macrohaplogroups, L, N, M, and R, and their corresponding haplogroups, according to universal nomenclature. The results obtained suggest an accuracy of 97.25% for the distribution of the 357 mtDNA sequences in the four macrohaplogroups and their corresponding haplogroups when compared with other mtDNA classification tools that require reference sequences and do not offer an analysis based on an evolutionary approach. These data are available online at http://biomedbiotec.encb.ipn.mx/VAMPhyRE/.}, }
@article {pmid33299013, year = {2020}, author = {Balzeau, A and Turq, A and Talamo, S and Daujeard, C and Guérin, G and Welker, F and Crevecoeur, I and Fewlass, H and Hublin, JJ and Lahaye, C and Maureille, B and Meyer, M and Schwab, C and Gómez-Olivencia, A}, title = {Pluridisciplinary evidence for burial for the La Ferrassie 8 Neandertal child.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21230}, pmid = {33299013}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Bone and Bones/metabolism ; Burial/*history/*methods ; Child, Preschool ; DNA, Mitochondrial/genetics ; Fossils ; France ; Geology ; History, Ancient ; Hominidae ; Humans ; Mass Spectrometry/methods ; Neanderthals/*psychology ; Paleontology ; }, abstract = {The origin of funerary practices has important implications for the emergence of so-called modern cognitive capacities and behaviour. We provide new multidisciplinary information on the archaeological context of the La Ferrassie 8 Neandertal skeleton (grand abri of La Ferrassie, Dordogne, France), including geochronological data -[14]C and OSL-, ZooMS and ancient DNA data, geological and stratigraphic information from the surrounding context, complete taphonomic study of the skeleton and associated remains, spatial information from the 1968-1973 excavations, and new (2014) fieldwork data. Our results show that a pit was dug in a sterile sediment layer and the corpse of a two-year-old child was laid there. A hominin bone from this context, identified through Zooarchaeology by Mass Spectrometry (ZooMS) and associated with Neandertal based on its mitochondrial DNA, yielded a direct [14]C age of 41.7-40.8 ka cal BP (95%), younger than the [14]C dates of the overlying archaeopaleontological layers and the OSL age of the surrounding sediment. This age makes the bone one of the most recent directly dated Neandertals. It is consistent with the age range for the Châtelperronian in the site and in this region and represents the third association of Neandertal taxa to Initial Upper Palaeolithic lithic technocomplex in Western Europe. A detailed multidisciplinary approach, as presented here, is essential to advance understanding of Neandertal behavior, including funerary practices.}, }
@article {pmid33296644, year = {2020}, author = {Jordan, B}, title = {[A poisoned gift].}, journal = {Medecine sciences : M/S}, volume = {36}, number = {12}, pages = {1233-1236}, doi = {10.1051/medsci/2020240}, pmid = {33296644}, issn = {1958-5381}, mesh = {Adaptor Proteins, Signal Transducing/genetics/metabolism ; Angiotensin-Converting Enzyme 2/metabolism ; Animals ; COVID-19/epidemiology/*genetics/pathology/therapy ; Case-Control Studies ; Chromosomes, Human, Pair 3/*genetics ; Europe/epidemiology ; Evolution, Molecular ; *Genetic Loci ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Hominidae/genetics ; Humans ; Membrane Glycoproteins/genetics/metabolism ; Membrane Transport Proteins/genetics/metabolism ; Neanderthals/*genetics ; Pandemics ; Polymorphism, Single Nucleotide ; Protein Binding ; Receptors, CCR/genetics ; Receptors, CXCR6/genetics ; SARS-CoV-2/metabolism/*pathogenicity ; Severity of Illness Index ; }, abstract = {GWAS analysis of severe Covid patients implicates a major locus on chromosome 3. The corresponding 50 kb segment appears to originate from Neanderthal/Sapiens crossings, raising interesting evolutionary questions.}, }
@article {pmid33290582, year = {2021}, author = {Brophy, JK and Moggi-Cecchi, J and Matthews, GJ and Bailey, SE}, title = {Comparative morphometric analyses of the deciduous molars of Homo naledi from the Dinaledi Chamber, South Africa.}, journal = {American journal of physical anthropology}, volume = {174}, number = {2}, pages = {299-314}, doi = {10.1002/ajpa.24190}, pmid = {33290582}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Fossils ; Hominidae/*anatomy &amp; histology/*classification ; Humans ; Molar/*anatomy &amp; histology ; Neanderthals/anatomy &amp; histology/classification ; Odontometry ; Principal Component Analysis ; South Africa ; }, abstract = {OBJECTIVES: The purpose of this study is to help elucidate the taxonomic relationship between Homo naledi and other hominins.<br><br>MATERIALS AND METHODS: Homo naledi deciduous maxillary and mandibular molars from the Dinaledi Chamber, South Africa were compared to those of Australopithecus africanus, Australopithecus afarensis, Paranthropus robustus, Paranthropus boisei, early Homo sp., Homo erectus, early Homo sapiens, Upper Paleolithic H. sapiens, recent southern African H. sapiens, and Neanderthals by means of morphometric analyses of crown outlines and relative cusp areas. The crown shapes were analyzed using elliptical Fourier analyses followed by principal component analyses (PCA). The absolute and relative cusp areas were obtained in ImageJ and compared using PCA and cluster analyses.<br><br>RESULTS: PCA suggests that the crown shapes and relative cusp areas of mandibular molars are more diagnostic than the maxillary molars. The H. naledi deciduous mandibular first and second molar (dm1 and dm2) do not have a strong affinity to any taxon in the comparative sample in all analyses. While the H. naledi dm2 plots as an outlier in the relative cusp analysis, the H. naledi specimen fall closest to Australopithecus due to their relatively large metaconid, a primitive trait for the genus Homo. Although useful for differentiating Neanderthals from recent southern African H. sapiens and UP H. sapiens, the PCA of the relative cusp areas suggests that the deciduous maxillary second molars (dm[2]) do not differentiate other groups. The three H. naledi dm[2] cuspal areas are variable and fall within the ranges of other Homo, as well as Australopithecus, and Paranthropus suggesting weak diagnostic utility.<br><br>DISCUSSION: This research provides another perspective on the morphology of, and variation within, H. naledi. The H. naledi deciduous molars do not consistently align with any genus or species in the comparative sample in either the crown shape or relative cusp analyses. This line of inquiry is consistent with other cranial and postcranial studies suggesting that H. naledi is unique.}, }
@article {pmid33278486, year = {2021}, author = {Wendt, FR and Pathak, GA and Overstreet, C and Tylee, DS and Gelernter, J and Atkinson, EG and Polimanti, R}, title = {Characterizing the effect of background selection on the polygenicity of brain-related traits.}, journal = {Genomics}, volume = {113}, number = {1 Pt 1}, pages = {111-119}, pmid = {33278486}, issn = {1089-8646}, support = {F32 MH122058/MH/NIMH NIH HHS/United States ; R21 DA047527/DA/NIDA NIH HHS/United States ; R21 DC018098/DC/NIDCD NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Brain/*metabolism ; *Genetic Background ; *Genetic Heterogeneity ; Humans ; Mental Disorders/diagnosis/*genetics ; *Multifactorial Inheritance ; Phenotype ; Polymorphism, Single Nucleotide ; *Selection, Genetic ; }, abstract = {BACKGROUND: Genome-wide association studies (GWAS) have demonstrated that psychopathology phenotypes are affected by many risk alleles with small effect (polygenicity). It is unclear how ubiquitously evolutionary pressures influence the genetic architecture of these traits.<br><br>METHODS: We partitioned SNP heritability to assess the contribution of background (BGS) and positive selection, Neanderthal local ancestry, functional significance, and genotype networks in 75 brain-related traits (8411&#xa0;&#x2264;&#xa0;N&#xa0;&#x2264;&#xa0;1,131,181, mean N&#xa0;=&#xa0;205,289). We applied binary annotations by dichotomizing each measure based on top 2%, 1%, and 0.5% of all scores genome-wide. Effect size distribution features were calculated using GENESIS. We tested the relationship between effect size distribution descriptive statistics and natural selection. In a subset of traits, we explore the inclusion of diagnostic heterogeneity (e.g., number of diagnostic combinations and total symptoms) in the tested relationship.<br><br>RESULTS: SNP-heritability was enriched (false discovery rate q&#xa0;<&#xa0;0.05) for loci with elevated BGS (7 phenotypes) and in genic (34 phenotypes) and loss-of-function (LoF)-intolerant regions (67 phenotypes). These effects were strongest in GWAS of schizophrenia (1.90-fold BGS, 1.16-fold genic, and 1.92-fold LoF), educational attainment (1.86-fold BGS, 1.12-fold genic, and 1.79-fold LoF), and cognitive performance (2.29-fold BGS, 1.12-fold genic, and 1.79-fold LoF). BGS (top 2%) significantly predicted effect size variance for trait-associated loci (&#x3c3;[2] parameter) in 75 brain-related traits (&#x3b2;&#xa0;=&#xa0;4.39&#xa0;&#xd7;&#xa0;10[-5], p&#xa0;=&#xa0;1.43&#xa0;&#xd7;&#xa0;10[-5], model r[2]&#xa0;=&#xa0;0.548). Considering the number of DSM-5 diagnostic combinations per psychiatric disorder improved model fit (&#x3c3;[2]&#xa0;~&#xa0;BTop2%&#xa0;&#xd7;&#xa0;Genic &#xd7; diagnostic combinations; model r[2]&#xa0;=&#xa0;0.661).<br><br>CONCLUSIONS: Brain-related phenotypes with larger variance in risk locus effect sizes are associated with loci under BGS. We show exploratory results suggesting that diagnostic complexity may also contribute to the increased polygenicity of psychiatric disorders.}, }
@article {pmid33276308, year = {2021}, author = {Shimelmitz, R and Groman-Yaroslavski, I and Weinstein-Evron, M and Rosenberg, D}, title = {A Middle Pleistocene abrading tool from Tabun Cave, Israel: A search for the roots of abrading technology in human evolution.}, journal = {Journal of human evolution}, volume = {150}, number = {}, pages = {102909}, doi = {10.1016/j.jhevol.2020.102909}, pmid = {33276308}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Caves ; *Cultural Evolution ; Israel ; *Neanderthals ; *Technology ; }, abstract = {During the reanalysis of the finds from Jelinek's and Ronen's excavations at Tabun Cave, Israel, we encountered a cobble bearing traces of mechanical alterations similar to those recorded on grinding tools. However, the artifact derives from the early layers of the Acheulo-Yabrudian complex of the late Lower Paleolithic (ca. 350 ka), a time with no evidence for grinding or abrasion. Accordingly, we sought to determine whether the traces on the artifact can be attributed to purposeful human action. We conducted a detailed use-wear analysis of the cobble and implemented an experimental program, gaining positive results for the hypothesis of purposeful human practice. We argue that the significance and novelty of early abrading technology is that it marks a new mode of raw material manipulation-one that is categorically different from other modes of tool use observed among earlier hominins or other primates and animals. Throughout the Early Pleistocene, use of stone tools was associated with vertical motions (battering, pounding, striking) or with the application of a thin or narrow working edge, leveled at cutting or scraping. Conversely, abrading consists in applying a wide working surface in a continuous sequence of horizontal motions, geared to modify or reduce the surfaces of a targeted material. The emergence of this technology joins additional behavioral changes recently identified and attributed to the Middle Pleistocene, illustrating the growing and diversifying capabilities of early hominins to harness technology to shape their environment.}, }
@article {pmid33264306, year = {2020}, author = {Riga, A and Boggioni, M and Papini, A and Buzi, C and Profico, A and Di Vincenzo, F and Marchi, D and Moggi-Cecchi, J and Manzi, G}, title = {In situ observations on the dentition and oral cavity of the Neanderthal skeleton from Altamura (Italy).}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0241713}, pmid = {33264306}, issn = {1932-6203}, mesh = {Animals ; Caves ; *Dentition ; *Fossils ; Hominidae/*anatomy &amp; histology ; Humans ; Italy ; Mandible/anatomy &amp; histology ; Maxilla/anatomy &amp; histology ; Mouth/physiology ; Neanderthals/*anatomy &amp; histology ; Paleodontology ; Skull/anatomy &amp; histology ; Tooth/anatomy &amp; histology ; }, abstract = {The Neanderthal specimen from Lamalunga Cave, near Altamura (Apulia, Italy), was discovered during a speleological survey in 1993. The specimen is one of the most complete fossil hominins in Europe and its state of preservation is exceptional, although it is stuck in calcareous concretions and the bones are mostly covered by calcite depositions. Nevertheless, it is possible to carry out some observations on craniodental features that have not previously been described. In this work, we present an account of the oral cavity, made possible by the use of a videoscope, which allowed us to reach some hidden parts of the mandible and palate. This is the first detailed overview of the teeth and maxillary bones of the Neanderthal skeleton from Altamura. The dentition is almost complete. However, two teeth (upper right P3 and upper left M1) were lost ante mortem and four teeth (lower right I1 and P3 and lower left I1 and I2) were lost most probably post mortem. Dental wear is marked. The erupted M3s and the inversion of the compensating curve of Wilson in the M1s and M2s but not in the M3s suggest that the individual is fully adult, but not old. Although most of the teeth have their roots exposed for several millimeters, the periodontal bone appears to be in good condition overall, except in correspondence of the two ante-mortem tooth losses. X-rays of the anterior teeth show a periapical lesion, probably linked to the advanced dental wear. We also observed a weak expression of taurodontism in the posterior dentition and the presence of a retromolar space, features consistent with an attribution to the Neanderthal hypodigm; this attribution is also supported by aspects of the cranial morphology, the morphometric analysis of the scapula and preliminary mtDNA data. There is also a well-developed palatine torus, to the best of our knowledge a feature not previously described in Neanderthals.}, }
@article {pmid33247712, year = {2021}, author = {Dannemann, M}, title = {The Population-Specific Impact of Neandertal Introgression on Human Disease.}, journal = {Genome biology and evolution}, volume = {13}, number = {1}, pages = {}, pmid = {33247712}, issn = {1759-6653}, mesh = {Alleles ; Animals ; Diabetes Mellitus, Type 2/genetics ; Disease/*genetics ; Evolution, Molecular ; Female ; Fossils ; Genetic Variation ; *Genome, Human ; *Genome-Wide Association Study ; Humans ; Japan ; Male ; Neanderthals/*genetics ; Phenotype ; Polymorphism, Single Nucleotide ; Whites/genetics ; }, abstract = {Since the discovery of admixture between modern humans and Neandertals, multiple studies investigated the effect of Neandertal-derived DNA on human disease and nondisease phenotypes. These studies have linked Neandertal ancestry to skin- and hair-related phenotypes, immunity, neurological, and behavioral traits. However, these inferences have so far been limited to cohorts with participants of European ancestry. Here, I analyze summary statistics from 40 disease GWAS (genome-wide association study) cohorts of ∼212,000 individuals provided by the Biobank Japan Project for phenotypic effects of Neandertal DNA. I show that Neandertal DNA is associated with autoimmune diseases, prostate cancer and type 2 diabetes. Many of these disease associations are linked to population-specific Neandertal DNA, highlighting the importance of studying a wider range of ancestries to characterize the phenotypic legacy of Neandertals in people today.}, }
@article {pmid33245148, year = {2021}, author = {Mineta, K and Goto, K and Gojobori, T and Alkuraya, FS}, title = {Indigenous Arabs have an intermediate frequency of a Neanderthal-derived COVID-19 risk haplotype compared with other world populations.}, journal = {Clinical genetics}, volume = {99}, number = {3}, pages = {484-485}, pmid = {33245148}, issn = {1399-0004}, mesh = {Alleles ; Animals ; Arabs/*genetics ; COVID-19/*genetics/virology ; *Gene Frequency ; *Genetic Predisposition to Disease ; Haplotypes/*genetics ; Heterozygote ; Homozygote ; Humans ; Neanderthals/*genetics ; Polymorphism, Single Nucleotide/genetics ; Population Groups/*genetics ; Risk Factors ; SARS-CoV-2/physiology ; Saudi Arabia ; }, }
@article {pmid33244047, year = {2020}, author = {Bardo, A and Moncel, MH and Dunmore, CJ and Kivell, TL and Pouydebat, E and Cornette, R}, title = {The implications of thumb movements for Neanderthal and modern human manipulation.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19323}, pmid = {33244047}, issn = {2045-2322}, support = {819960/ERC_/European Research Council/International ; }, mesh = {Adult ; Animals ; Anthropology, Physical ; Biological Evolution ; Female ; Fossils/anatomy &amp; histology ; Hand Strength/physiology ; History, 21st Century ; History, Ancient ; Humans ; Imaging, Three-Dimensional ; Male ; Metacarpal Bones/anatomy &amp; histology ; Models, Biological ; Movement ; Neanderthals/*anatomy &amp; histology/*physiology ; Species Specificity ; Thumb/*anatomy &amp; histology/*physiology ; Trapezium Bone/anatomy &amp; histology ; }, abstract = {Much research has debated the technological abilities of Neanderthals relative to those of early modern humans, with a particular focus on subtle differences in thumb morphology and how this may reflect differences in manipulative behaviors in these two species. Here, we provide a novel perspective on this debate through a 3D geometric morphometric analysis of shape covariation between the trapezial and proximal first metacarpal articular surfaces of Neanderthals (Homo neanderthalensis) in comparison to early and recent humans (Homo sapiens). Results show a distinct pattern of shape covariation in Neanderthals, consistent with more extended and adducted thumb postures that may reflect habitual use of grips commonly used for hafted tools. Both Neanderthals and recent humans demonstrate high intraspecific variation in shape covariation. This intraspecific variation is likely the result of genetic and/or developmental differences, but may also reflect, in part, differing functional requirements imposed by the use of varied tool-kits. These results underscore the importance of holistic joint shape analysis for understanding the functional capabilities and evolution of the modern human thumb.}, }
@article {pmid33230523, year = {2021}, author = {Aarts, JMMJG and Alink, GM and Franssen, HJ and Roebroeks, W}, title = {Evolution of Hominin Detoxification: Neanderthal and Modern Human Ah Receptor Respond Similarly to TCDD.}, journal = {Molecular biology and evolution}, volume = {38}, number = {4}, pages = {1292-1305}, pmid = {33230523}, issn = {1537-1719}, mesh = {Animals ; Cytochrome P-450 CYP1A1/*metabolism ; Environmental Pollutants/*metabolism ; *Evolution, Molecular ; HeLa Cells ; Hep G2 Cells ; Humans ; Inactivation, Metabolic/genetics ; Neanderthals/*genetics/metabolism ; Polychlorinated Dibenzodioxins/*metabolism ; Receptors, Aryl Hydrocarbon/chemistry/*genetics/metabolism ; }, abstract = {In studies of hominin adaptations to fire use, the role of the aryl hydrocarbon receptor (AHR) in the evolution of detoxification has been highlighted, including statements that the modern human AHR confers a significantly better capacity to deal with toxic smoke components than the Neanderthal AHR. To evaluate this, we compared the AHR-controlled induction of cytochrome P4501A1 (CYP1A1) mRNA in HeLa human cervix epithelial adenocarcinoma cells transfected with an Altai-Neanderthal or a modern human reference AHR expression construct, and exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). We compared the complete AHR mRNA sequences including the untranslated regions (UTRs), maintaining the original codon usage. We observe no significant difference in CYP1A1 induction by TCDD between Neanderthal and modern human AHR, whereas a 150-1,000 times difference was previously reported in a study of the AHR coding region optimized for mammalian codon usage and expressed in rat cells. Our study exemplifies that expression in a homologous cellular background is of major importance to determine (ancient) protein activity. The Neanderthal and modern human dose-response curves almost coincide, except for a slightly higher extrapolated maximum for the Neanderthal AHR, possibly caused by a 5'-UTR G-variant known from modern humans (rs7796976). Our results are strongly at odds with a major role of the modern human AHR in the evolution of hominin detoxification of smoke components and consistent with our previous study based on 18 relevant genes in addition to AHR, which concluded that efficient detoxification alleles are more dominant in ancient hominins, chimpanzees, and gorillas than in modern humans.}, }
@article {pmid33226710, year = {2021}, author = {Weyrich, LS}, title = {The evolutionary history of the human oral microbiota and its implications for modern health.}, journal = {Periodontology 2000}, volume = {85}, number = {1}, pages = {90-100}, doi = {10.1111/prd.12353}, pmid = {33226710}, issn = {1600-0757}, mesh = {Diet ; Humans ; *Microbiota/genetics ; *Mouth Diseases ; Oral Health ; }, abstract = {Numerous biological and cultural factors influence the microbial communities (microbiota) that inhabit the human mouth, including diet, environment, hygiene, physiology, health status, genetics, and lifestyle. As oral microbiota can underpin oral and systemic diseases, tracing the evolutionary history of oral microbiota and the factors that shape its origins will unlock information to mitigate disease today. Despite this, the origins of many oral microbes remain unknown, and the key factors in the past that shaped our oral microbiota are only now emerging. High throughput DNA sequencing of oral microbiota using ancient DNA and comparative anthropological methodologies has been employed to investigate oral microbiota origins, revealing a complex, rich history. Here, I review the current literature on the factors that shaped and guided oral microbiota evolution, both in Europe and globally. In Europe, oral microbiota evolution was shaped by interactions with Neandertals, the adaptation of farming, widespread integration of industrialization, and postindustrial lifestyles that emerged after World War II. Globally, evidence for a multitude of different oral microbiota histories is emerging, likely supporting dissimilarities in modern oral health across discrete human populations. I highlight how these evolutionary changes are linked to the development of modern oral diseases and discuss the remaining factors that need to be addressed to improve this embryonic field of research. I argue that understanding the evolutionary history of our oral microbiota is necessary to identify new treatment and prevention options to improve oral and systemic health in the future.}, }
@article {pmid33218283, year = {2021}, author = {Gregory, MD and Kippenhan, JS and Kohn, P and Eisenberg, DP and Callicott, JH and Kolachana, B and Berman, KF}, title = {Neanderthal-Derived Genetic Variation is Associated with Functional Connectivity in the Brains of Living Humans.}, journal = {Brain connectivity}, volume = {11}, number = {1}, pages = {38-44}, pmid = {33218283}, issn = {2158-0022}, support = {ZIA MH002942/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Animals ; Brain ; Genetic Variation/genetics ; Humans ; Magnetic Resonance Imaging ; *Neanderthals/genetics ; }, abstract = {Aim: To determine whether Neanderthal-derived genetic variation relates to functional connectivity patterns in the brains of living modern humans. Introduction: Nearly 50,000 years ago, Neanderthals interbred with ancestors of modern humans, imparting a genetic legacy that lives on today. The vestiges of this Neanderthal-derived genetic variation have been previously shown to be enriched in genes coding for neurogenesis and myelination and to alter skull shape and brain structure in living people. Materials and Methods: Using two independent cohorts totaling 553 healthy individuals, we employed multivariate distance matrix regression (MDMR) to determine whether any brain areas exhibited whole-brain functional connectivity patterns that significantly related to the degree of Neanderthal introgression. Identified clusters were then used as regions of interest in follow-up seed-based functional connectivity analyses to determine the connectivity patterns driving the relationships. Results: The MDMR analysis revealed that the percentage of Neanderthal-originating polymorphisms was significantly associated with the functional connectivity patterns of an area of the intraparietal sulcus (IPS) that was nearly identical in both cohorts. Using these IPS clusters as regions of interest in seed-based connectivity analyses, we found, again in both cohorts, that individuals with a higher proportion of Neanderthal-derived genetic variation showed increased IPS functional connectivity with visual processing regions, but decreased IPS connectivity with regions underlying social cognition. Conclusions: These findings demonstrate that the remnants of Neanderthal admixture continue to influence human brain function today, in ways that are consistent with anthropological conceptualizations of Neanderthal phenotypes, including the possibility that Neanderthals may have depended upon visual processing capabilities at the expense of social cognition, and this may have contributed to the extinction of this species through reduced cultural maintenance and inability to cope with fluctuating resources. This and other studies capitalizing on the emerging science surrounding ancient DNA provide a window through which to view an ancient lineage long past.}, }
@article {pmid33170414, year = {2020}, author = {Madison, P}, title = {Characterized by Darkness: Reconsidering the Origins of the Brutish Neanderthal.}, journal = {Journal of the history of biology}, volume = {53}, number = {4}, pages = {493-519}, pmid = {33170414}, issn = {1573-0387}, support = {60669//John Templeton Foundation/International ; Center for Biology//School of Life Sciences, Arizona State University/International ; Society//School of Life Sciences, Arizona State University/International ; }, abstract = {The extinct human relatives known as Neanderthals (Homo neanderthalensis) have long been described as brutish and dumb. This conception is often traced to paleontologist Marcellin Boule (1861-1942), who published a detailed analysis on a Neanderthal skeleton in the early twentieth century. The conventional historical narrative claims that Boule made an error in his analysis, causing the Neanderthals to be considered brutish. This essay challenges the narrative of "Boule's error," arguing instead that the brutish Neanderthal concept originated much earlier in the history of Neanderthal research and was, in fact, an invention of the earliest analyses of the first specimen recognized as a Neanderthal in the mid-nineteenth century. I argue that temporally relocating this conception of Neanderthals allows for a better understanding of the interconnected nature of the study of fossil humans and the science of living human races during the nineteenth century. This new view of the brutish Neanderthal sheds light on the earliest phases of the science that became paleoanthropology, while examining the racial, cultural, and political attitudes about race and extinction that accompanied the science at that time. By inspecting the ways in which the Neanderthals' image was a product of a particular time and place, we gain a perspective that provides a new basis for thinking about the conceptions of hominin fossil species.}, }
@article {pmid33139541, year = {2020}, author = {Nava, A and Lugli, F and Romandini, M and Badino, F and Evans, D and Helbling, AH and Oxilia, G and Arrighi, S and Bortolini, E and Delpiano, D and Duches, R and Figus, C and Livraghi, A and Marciani, G and Silvestrini, S and Cipriani, A and Giovanardi, T and Pini, R and Tuniz, C and Bernardini, F and Dori, I and Coppa, A and Cristiani, E and Dean, C and Bondioli, L and Peresani, M and Müller, W and Benazzi, S}, title = {Early life of Neanderthals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {46}, pages = {28719-28726}, pmid = {33139541}, issn = {1091-6490}, mesh = {Animals ; Dental Enamel/chemistry/*growth &amp; development ; Humans ; Infant ; Infant, Newborn ; Neanderthals/*growth &amp; development ; *Weaning ; }, abstract = {The early onset of weaning in modern humans has been linked to the high nutritional demand of brain development that is intimately connected with infant physiology and growth rate. In Neanderthals, ontogenetic patterns in early life are still debated, with some studies suggesting an accelerated development and others indicating only subtle differences vs. modern humans. Here we report the onset of weaning and rates of enamel growth using an unprecedented sample set of three late (∼70 to 50 ka) Neanderthals and one Upper Paleolithic modern human from northeastern Italy via spatially resolved chemical/isotopic analyses and histomorphometry of deciduous teeth. Our results reveal that the modern human nursing strategy, with onset of weaning at 5 to 6 mo, was present among these Neanderthals. This evidence, combined with dental development akin to modern humans, highlights their similar metabolic constraints during early life and excludes late weaning as a factor contributing to Neanderthals' demise.}, }
@article {pmid33137550, year = {2020}, author = {Palancar, CA and Torres-Tamayo, N and García-Martínez, D and García-Tabernero, A and Rosas, A and Bastir, M}, title = {Comparative anatomy and 3D geometric morphometrics of the El Sidrón atlases (C1).}, journal = {Journal of human evolution}, volume = {149}, number = {}, pages = {102897}, doi = {10.1016/j.jhevol.2020.102897}, pmid = {33137550}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Cervical Atlas/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Spain ; }, abstract = {The first cervical vertebra (atlas, C1) is an important element of the vertebral column because it connects the cranial base with the cervical column, thus helping to maintain head posture and contributing to neck mobility. However, few atlases are preserved in the fossil record because of the fragility of this vertebra. Consequently, only eight well-preserved atlases from adult Neandertals have been recovered and described. Here, we present nine new atlas remains from the El Sidrón Neandertal site (Asturias, Spain), two of which (SD-1643 and SD-1605/1595) are sufficiently well preserved to allow for a detailed comparative and three-dimensional geometric morphometric analysis. We compared standard linear measurements of SD-1643 and SD-1605/1595 with those of other Neandertal atlases and carried out three-dimensional geometric morphometric analyses to compare size and shape of SD-1643 and SD-1605/1595 with those of 28 Pan (Pan troglodytes and Pan paniscus), a broad comparative sample of 55 anatomically modern humans from African and European populations, and other fossil hominins (Neandertals, Homo antecessor, Paranthropus boisei). The El Sidrón atlas fossils show typical features of the Neandertal atlas morphology, such as caudal projection of the anterior tubercle, gracility of both the posterior tubercle and the tuberosity for the insertion of the transverse ligament, and an anteroposteriorly elongated neural canal. Furthermore, when compared with atlases from the other taxa, Neandertals exhibit species-specific features of atlas morphology including a relatively lower lateral mass height, relatively narrower transverse foramina, and flatter and more horizontally oriented articular facets. Some of these features fit with previous suggestions of shorter overall length of the cervical spine and potential differences in craniocervical posture and mobility. Our results may support a different spinopelvic alignment in this species, as the atlas morphology suggests reduced cervical lordosis.}, }
@article {pmid33130632, year = {2020}, author = {Bruner, E and Lombard, M}, title = {The skull from Florisbad: a paleoneurological report.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {98}, number = {}, pages = {}, doi = {10.4436/JASS.98014}, pmid = {33130632}, issn = {2037-0644}, mesh = {Animals ; Biological Evolution ; Cephalometry ; *Fossils ; Hominidae/*anatomy &amp; histology ; Humans ; Neanderthals/anatomy &amp; histology ; Paleontology ; Skull/*anatomy &amp; histology ; South Africa ; }, abstract = {The Florisbad fossil cranium was found in South Africa in 1932. Different authors proposed a taxonomic affinity with early Homo sapiens, Neandertals or late Homo heidelbergensis. Here, we review its neurocranial morphology, to supply an updated perspective on its paleoneurological features. The curvature of the frontal squama is definitely within modern human variation, although the anterior cranial fossa is very broad, comparable to that of the Neandertals. In contrast, the parietal lobe and the vascular networks are more similar to the morphology observed in more archaic human species, such as Homo heidelbergensis. The endocranial anatomy of the Florisbad skull displays a mosaic of derived and plesiomorphic features, which makes this fossil compatible with distinct phylogenetic scenarios. None of these traits are, however, strictly diagnostic in terms of taxonomy. This specimen is central to the question on the possible anagenetic evolution from Homo heidelbergensis sensu lato to modern humans.}, }
@article {pmid33122381, year = {2020}, author = {Zhang, D and Xia, H and Chen, F and Li, B and Slon, V and Cheng, T and Yang, R and Jacobs, Z and Dai, Q and Massilani, D and Shen, X and Wang, J and Feng, X and Cao, P and Yang, MA and Yao, J and Yang, J and Madsen, DB and Han, Y and Ping, W and Liu, F and Perreault, C and Chen, X and Meyer, M and Kelso, J and Pääbo, S and Fu, Q}, title = {Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau.}, journal = {Science (New York, N.Y.)}, volume = {370}, number = {6516}, pages = {584-587}, doi = {10.1126/science.abb6320}, pmid = {33122381}, issn = {1095-9203}, mesh = {Animals ; *Caves ; DNA, Ancient/*isolation &amp; purification ; DNA, Mitochondrial/genetics ; Geologic Sediments/*chemistry ; Hominidae/*classification/*genetics ; Humans ; Phylogeny ; Tibet ; }, abstract = {A late Middle Pleistocene mandible from Baishiya Karst Cave (BKC) on the Tibetan Plateau has been inferred to be from a Denisovan, an Asian hominin related to Neanderthals, on the basis of an amino acid substitution in its collagen. Here we describe the stratigraphy, chronology, and mitochondrial DNA extracted from the sediments in BKC. We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand years ago (ka) and possibly as recently as ~45 ka. The long-term occupation of BKC by Denisovans suggests that they may have adapted to life at high altitudes and may have contributed such adaptations to modern humans on the Tibetan Plateau.}, }
@article {pmid33111974, year = {2021}, author = {Cofran, Z and Boone, M and Petticord, M}, title = {Virtually estimated endocranial volumes of the Krapina Neandertals.}, journal = {American journal of physical anthropology}, volume = {174}, number = {1}, pages = {117-128}, doi = {10.1002/ajpa.24165}, pmid = {33111974}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Cephalometry/*methods ; Female ; Fossils ; Hominidae/anatomy &amp; histology ; Humans ; Imaging, Three-Dimensional ; Male ; Neanderthals/*anatomy &amp; histology ; Skull/*anatomy &amp; histology/*diagnostic imaging ; }, abstract = {OBJECTIVES: The Krapina rock shelter has yielded a large assemblage of early Neandertals. Although endocranial volume (ECV) has been estimated for four individuals from the site, several published values that appear in the literature warrant revisiting.<br><br>MATERIALS AND METHODS: We used virtual methods, including high-resolution surface models of fossils and 3D geometric morphometrics, to reconstruct endocasts and estimate ECV for five Krapina crania. We generated 10 reconstructions of each endocast to quantify missing data uncertainty. To assess the method and our ECV estimates, we applied these techniques to the Spy II Neandertal, and estimated ECV of a human reference endocast simulating the missing data of the Krapina fossils.<br><br>RESULTS: We obtained an average ECV estimate of 1,526&#x2009;cm[3] for Spy II, consistent with previous research. Estimated ECV of juveniles Krapina 1 and 2 average 1,419 and 1,286&#x2009;cm[3] , respectively. Estimates for the relatively complete adults Krapina 3 and 6 range from 1,247 to 1,310&#x2009;cm[3] and 1,135 to 1,207&#x2009;cm[3] , respectively, while the more fragmentary Krapina 5 averaged 1,397&#x2009;cm[3] . The missing data simulation suggests more fragmentary crania yield more uncertain and possibly overestimated ECVs.<br><br>CONCLUSIONS: We have provided new estimates of brain size of the Krapina Neandertals, including the first estimates for Krapina 2. Brain size at Krapina was similar to other pre-W&#xfc;rm Neandertals, within the range of but lower than the average of later Neandertals. Although the virtual approach overcomes many challenges of fossil preservation, our results are nevertheless subject to future revision.}, }
@article {pmid33106620, year = {2020}, author = {Luo, Y}, title = {Neanderthal DNA highlights complexity of COVID risk factors.}, journal = {Nature}, volume = {587}, number = {7835}, pages = {552-553}, pmid = {33106620}, issn = {1476-4687}, mesh = {Betacoronavirus ; COVID-19 ; *Coronavirus Infections/epidemiology ; DNA ; Humans ; *Neanderthals/genetics ; *Pandemics ; *Pneumonia, Viral ; Risk Factors ; SARS-CoV-2 ; }, }
@article {pmid33077870, year = {2021}, author = {Yang, S and Varghese, AM and Sood, N and Chiattone, C and Akinola, NO and Huang, X and Gale, RP}, title = {Ethnic and geographic diversity of chronic lymphocytic leukaemia.}, journal = {Leukemia}, volume = {35}, number = {2}, pages = {433-439}, pmid = {33077870}, issn = {1476-5551}, mesh = {Aged ; Asian Americans/genetics/statistics &amp; numerical data ; Ethnicity/*genetics/*statistics &amp; numerical data ; Far East/epidemiology ; Female ; *Genetic Predisposition to Disease ; *Genetic Variation ; *Genetics, Population ; Genome, Human ; Geography ; Global Health ; Humans ; Incidence ; Leukemia, Lymphocytic, Chronic, B-Cell/*epidemiology/genetics/pathology ; Male ; Middle Aged ; Risk Factors ; Whites/genetics/statistics &amp; numerical data ; }, abstract = {East Asians, Asian Indians and Amerindians have a five to ten-fold lower age-adjusted incidence rate (AAIR) of chronic lymphocytic leukaemia (CLL) compared with persons of predominately European descent. The data we review suggest a genetic rather than environmental basis for this discordance. All these populations arose from a common African Black ancestor but different clades have different admixture with archaic hominins including Neanderthals, Denisovans and Homo erectus, which may explain different CLL incidences. There are also some differences in clinical laboratory and molecular co-variates of CLL between these populations. Because the true age-adjusted incidence rate in African Blacks is unknown it is not possible to determine whether modern Europeans acquired susceptibility to CLL or the other populations lost susceptibility and/or developed resistance to developing CLL. We also found other B-cell lymphomas and T- and NK-cell cancers had different incidences in the populations we studied. These data provide clues to determining the cause(s) of CLL.}, }
@article {pmid33043635, year = {2020}, author = {}, title = {Risk Variant for Severe COVID-19 Inherited from Neanderthals.}, journal = {American journal of medical genetics. Part A}, volume = {182}, number = {10}, pages = {2203-2204}, doi = {10.1002/ajmg.a.61247}, pmid = {33043635}, issn = {1552-4833}, mesh = {Animals ; Betacoronavirus/*genetics ; COVID-19 ; Coronavirus Infections/epidemiology/*virology ; Female ; Haplotypes ; Humans ; Male ; Neanderthals ; *Pandemics ; Pneumonia, Viral/epidemiology/*virology ; Risk Factors ; SARS-CoV-2 ; Sex Factors ; }, }
@article {pmid33039881, year = {2020}, author = {Pan, L and Dumoncel, J and Mazurier, A and Zanolli, C}, title = {Hominin diversity in East Asia during the Middle Pleistocene: A premolar endostructural perspective.}, journal = {Journal of human evolution}, volume = {148}, number = {}, pages = {102888}, doi = {10.1016/j.jhevol.2020.102888}, pmid = {33039881}, issn = {1095-8606}, mesh = {Animals ; Bicuspid ; Far East ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; }, abstract = {Following the recent studies of East Asian mid-Middle to early Late Pleistocene hominin material, a large spectrum of morphological diversity has been recognized and the coexistence of archaic ('Homo erectus-like') and derived ('modern-like') dental morphological patterns has been highlighted. In fact, for most of these Chinese fossils, generally categorized as 'archaic Homo sapiens' or 'post-H. erectus Homo', the taxonomic attribution is a matter of contention. With the help of μCT techniques and a deformation-based 3D geometric morphometric approach, we focused on the morphological variation in the enamel-dentine junction (EDJ) of 18 upper and lower premolars from Chinese Middle Pleistocene hominins. We then compared our results with a number of fossil and modern human groups, including Early Pleistocene H. erectus from Sangiran; late Early Pleistocene hominins from Tighenif, Algeria; classic Neanderthals; and modern humans. Our results highlight an evolutionary/chronological trend of crown base reduction, elevation of EDJ topography, and EDJ surface simplification in the hominin groups studied here. Moreover, this study brings insights to the taxonomy/phylogeny of 6 late Middle Pleistocene specimens whose evolutionary placement has been debated for decades. Among these specimens, Changyang premolars show features that can be aligned with the Asian H. erectus hypodigm, whereas Panxian Dadong and Tongzi premolars are more similar to Late Pleistocene Homo. Compared with early to mid-Middle Pleistocene hominins in East Asia, late Middle Pleistocene hominins evince an enlarged morphological variation. A persistence of archaic morphotypes and possible admixture among populations during the late Middle Pleistocene are discussed.}, }
@article {pmid33028520, year = {2020}, author = {García-Martínez, D and Bastir, M and Gómez-Olivencia, A and Maureille, B and Golovanova, L and Doronichev, V and Akazawa, T and Kondo, O and Ishida, H and Gascho, D and Zollikofer, CPE and de León, MP and Heuzé, Y}, title = {Early development of the Neanderthal ribcage reveals a different body shape at birth compared to modern humans.}, journal = {Science advances}, volume = {6}, number = {41}, pages = {}, pmid = {33028520}, issn = {2375-2548}, abstract = {Ontogenetic studies provide clues for understanding important paleobiological aspects of extinct species. When compared to that of modern humans, the adult Neanderthal thorax was shorter, deeper, and wider. This is related to the wide Neanderthal body and is consistent with their hypothetical large requirements for energy and oxygen. Whether these differences were already established at birth or appeared later during development is unknown. To delve into this question, we use virtual reconstruction tools and geometric morphometrics to recover the 3D morphology of the ribcages of four Neanderthal individuals from birth to around 3 years old: Mezmaiskaya 1, Le Moustier 2, Dederiyeh 1, and Roc de Marsal. Our results indicate that the comparatively deep and short ribcage of the Neanderthals was already present at birth, as were other skeletal species-specific traits. This morphology possibly represents the plesiomorphic condition shared with Homo erectus, and it is likely linked to large energetic requirements.}, }
@article {pmid32998156, year = {2020}, author = {Zeberg, H and Pääbo, S}, title = {The major genetic risk factor for severe COVID-19 is inherited from Neanderthals.}, journal = {Nature}, volume = {587}, number = {7835}, pages = {610-612}, pmid = {32998156}, issn = {1476-4687}, mesh = {Animals ; Asia/ethnology ; COVID-19/complications/*genetics/*physiopathology ; Case-Control Studies ; Chromosomes, Human, Pair 3/genetics ; Europe/ethnology ; *Genetic Predisposition to Disease ; Genetic Variation/genetics ; Genome-Wide Association Study ; Haplotypes/genetics ; Hospitalization ; Humans ; Linkage Disequilibrium/genetics ; Multigene Family/genetics ; Neanderthals/*genetics ; Phylogeny ; Severe Acute Respiratory Syndrome/complications/genetics/physiopathology ; }, abstract = {A recent genetic association study[1] identified a gene cluster on chromosome 3 as a risk locus for respiratory failure after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A separate study (COVID-19 Host Genetics Initiative)[2] comprising 3,199 hospitalized patients with coronavirus disease 2019 (COVID-19) and control individuals showed that this cluster is the major genetic risk factor for severe symptoms after SARS-CoV-2 infection and hospitalization. Here we show that the risk is conferred by a genomic segment of around 50 kilobases in size that is inherited from Neanderthals and is carried by around 50% of people in south Asia and around 16% of people in Europe.}, }
@article {pmid32989161, year = {2020}, author = {Haws, JA and Benedetti, MM and Talamo, S and Bicho, N and Cascalheira, J and Ellis, MG and Carvalho, MM and Friedl, L and Pereira, T and Zinsious, BK}, title = {The early Aurignacian dispersal of modern humans into westernmost Eurasia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {41}, pages = {25414-25422}, pmid = {32989161}, issn = {1091-6490}, mesh = {*Archaeology ; *Demography ; Emigration and Immigration/history ; *Fossils ; History, Ancient ; Humans ; Portugal ; Radiometric Dating ; }, abstract = {Documenting the first appearance of modern humans in a given region is key to understanding the dispersal process and the replacement or assimilation of indigenous human populations such as the Neanderthals. The Iberian Peninsula was the last refuge of Neanderthal populations as modern humans advanced across Eurasia. Here we present evidence of an early Aurignacian occupation at Lapa do Picareiro in central Portugal. Diagnostic artifacts were found in a sealed stratigraphic layer dated 41.1 to 38.1 ka cal BP, documenting a modern human presence on the western margin of Iberia ∼5,000 years earlier than previously known. The data indicate a rapid modern human dispersal across southern Europe, reaching the westernmost edge where Neanderthals were thought to persist. The results support the notion of a mosaic process of modern human dispersal and replacement of indigenous Neanderthal populations.}, }
@article {pmid32975051, year = {2021}, author = {Chirchir, H}, title = {Trabecular bone in domestic dogs and wolves: Implications for understanding human self-domestication.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {304}, number = {1}, pages = {31-41}, doi = {10.1002/ar.24510}, pmid = {32975051}, issn = {1932-8494}, mesh = {Animals ; Behavior, Animal/physiology ; Cancellous Bone/*anatomy &amp; histology/diagnostic imaging ; Dogs ; *Domestication ; Femur Head/*anatomy &amp; histology/diagnostic imaging ; Tibia/*anatomy &amp; histology/diagnostic imaging ; Wolves ; X-Ray Microtomography ; }, abstract = {The process of domestication is complex and results in significant morphological, cognitive, and physiological changes. In canids, some of the traits indicative of domestication of domestic dogs compared to their wild counterparts the wolves are prosociality toward humans, reduced stress hormone levels, and reduced cranial capacity. Research suggests that selection for prosociality among dogs resulted in morphological changes such as reduction in cranial capacity, juvenilization of the face, and overall gracile morphology. Interestingly, similar features have been described in modern humans compared to extinct species of Homo, for example, Neanderthals. Therefore, the human self-domestication hypothesis has been proposed to partially explain the gracile modern human skeleton. Specifically, that as modern humans settled in communities, there was increased selection for prosociality (intergroup cooperation); and one of the by-products of this selection was the evolution of a gracile skeleton, including a slight reduction in cranial capacity, reduced brow ridge and tooth size, and low trabecular bone fraction (TBF). However, TBF variation has not been tested between domestic dogs and wolves, who underwent self-domestication. Thus, this study tests the hypothesis that dogs have low TBF as a consequence of domestication compared to their wild counterparts, the wolves, by comparing TBF in the hindlimbs-proximal femur and distal tibia- of the two species. Wilcoxon rank sum tests show that dogs have lower TBF values than wolves in both elements. These preliminary results add to the literature documenting changes in self-domesticated species and provide a potential analog to further the understanding of self-domestication.}, }
@article {pmid32973032, year = {2020}, author = {Petr, M and Hajdinjak, M and Fu, Q and Essel, E and Rougier, H and Crevecoeur, I and Semal, P and Golovanova, LV and Doronichev, VB and Lalueza-Fox, C and de la Rasilla, M and Rosas, A and Shunkov, MV and Kozlikin, MB and Derevianko, AP and Vernot, B and Meyer, M and Kelso, J}, title = {The evolutionary history of Neanderthal and Denisovan Y chromosomes.}, journal = {Science (New York, N.Y.)}, volume = {369}, number = {6511}, pages = {1653-1656}, doi = {10.1126/science.abb6460}, pmid = {32973032}, issn = {1095-9203}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Chromosomes, Human, Y/genetics ; DNA, Ancient ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Humans ; *Life History Traits ; Male ; Neanderthals/classification/*genetics ; Phylogeny ; Y Chromosome/*genetics ; }, abstract = {Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.}, }
@article {pmid32973019, year = {2020}, author = {Schierup, MH}, title = {The last pieces of a puzzling early meeting.}, journal = {Science (New York, N.Y.)}, volume = {369}, number = {6511}, pages = {1565-1566}, doi = {10.1126/science.abe2766}, pmid = {32973019}, issn = {1095-9203}, mesh = {Animals ; Biological Evolution ; *Neanderthals ; Y Chromosome ; }, }
@article {pmid32964411, year = {2020}, author = {Wei, P and Lu, H and Carlson, KJ and Zhang, H and Hui, J and Zhu, M and He, K and Jashashvili, T and Zhang, X and Yuan, H and Xing, S}, title = {The upper limb skeleton and behavioral lateralization of modern humans from Zhaoguo Cave, southwestern China.}, journal = {American journal of physical anthropology}, volume = {173}, number = {4}, pages = {671-696}, doi = {10.1002/ajpa.24147}, pmid = {32964411}, issn = {1096-8644}, mesh = {Adaptation, Physiological/*physiology ; Adult ; Animals ; Burial/history ; Caves ; China/ethnology ; Female ; Fossils ; History, Ancient ; Humans ; Humerus/*anatomy &amp; histology/*pathology ; Male ; Neanderthals ; }, abstract = {OBJECTIVES: Aims of the study are to initially describe and comparatively evaluate the morphology of the new Zhaoguo M1 upper limb remains, and contextualize upper limb functional adaptations among those of other worldwide Upper Paleolithic (UP) humans to make inferences about subsistence-related activity patterns in southwestern China at the Pleistocene-Holocene boundary.<br><br>MATERIALS AND METHODS: The preserved Zhaoguo M1 skeletal remains include paired humeri, ulnae, and radii, among others. These specimens were scanned using micro-computed tomography to evaluate internal structural properties, while external osteometric dimensions of the Zhaoguo M1 upper limb elements also were acquired. Both sets of measurements were compared to published data on Neandertals, and Middle and Upper Paleolithic modern humans.<br><br>RESULTS: The upper limb elements of Zhaoguo M1 display a suite of characteristics that generally resemble those of other contemporary Late UP (LUP) modern humans, while robusticity indices generally fall within the upper range of LUP variation. The Zhaoguo M1 upper limb elements display fewer traits resembling those of late archaic humans. The Zhaoguo M1 individual exhibits diaphyseal asymmetry in several upper limb elements suggesting left hand dominance. When evaluating the full range of magnitudes of humeral bilateral asymmetry in the comparative sample, Zhaoguo M1 falls at the lower end overall, but yet is relatively higher than contemporary LUP modern humans specifically from East Eurasia.<br><br>DISCUSSION: The Zhaoguo M1 individual suggests typical LUP modern human upper limb morphology persisted in southwest China until the end of the last glacial period. Upper limb bone asymmetry of Zhaoguo M1 also indicates that behavioral activities attributed to a hunter-gatherer tradition apparently extended through the Pleistocene-Holocene transition in this region.}, }
@article {pmid32963029, year = {2020}, author = {Bokelmann, L and Glocke, I and Meyer, M}, title = {Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples.}, journal = {Genome research}, volume = {30}, number = {10}, pages = {1449-1457}, pmid = {32963029}, issn = {1549-5469}, mesh = {Animals ; Cell-Free Nucleic Acids/blood ; Cytosine/metabolism ; DNA/blood ; DNA, Ancient/*chemistry ; Deamination ; High-Throughput Nucleotide Sequencing ; Humans ; Neanderthals/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Extensive manipulations involved in the preparation of DNA samples for sequencing have hitherto made it impossible to determine the precise structure of double-stranded DNA fragments being sequenced, such as the presence of blunt ends, single-stranded overhangs, or single-strand breaks. We here describe MatchSeq, a method that combines single-stranded DNA library preparation from diluted DNA samples with computational sequence matching, allowing the reconstruction of double-stranded DNA fragments on a single-molecule level. The application of MatchSeq to Neanderthal DNA, a particularly complex source of degraded DNA, reveals that 1- or 2-nt overhangs and blunt ends dominate the ends of ancient DNA molecules and that short gaps exist, which are predominantly caused by the loss of individual purines. We further show that deamination of cytosine to uracil occurs in both single- and double-stranded contexts close to the ends of molecules, and that single-stranded parts of DNA fragments are enriched in pyrimidines. MatchSeq provides unprecedented resolution for interrogating the structures of fragmented double-stranded DNA and can be applied to fragmented double-stranded DNA isolated from any biological source. The method relies on well-established laboratory techniques and can easily be integrated into routine data generation. This possibility is shown by the successful reconstruction of double-stranded DNA fragments from previously published single-stranded sequence data, allowing a more comprehensive characterization of the biochemical properties not only of ancient DNA but also of cell-free DNA from human blood plasma, a clinically relevant marker for the diagnosis and monitoring of disease.}, }
@article {pmid32927399, year = {2020}, author = {Bailey, SE and Sorrentino, R and Mancuso, G and Hublin, JJ and Benazzi, S}, title = {Taxonomic differences in deciduous lower first molar crown outlines of Homo sapiens and Homo neanderthalensis.}, journal = {Journal of human evolution}, volume = {147}, number = {}, pages = {102864}, doi = {10.1016/j.jhevol.2020.102864}, pmid = {32927399}, issn = {1095-8606}, mesh = {Animals ; Fossils ; Humans ; Molar/*anatomy &amp; histology ; Neanderthals/anatomy &amp; histology/*classification ; Tooth Crown/*anatomy &amp; histology ; Tooth, Deciduous/*anatomy &amp; histology ; }, abstract = {Recent studies have demonstrated that the outline shapes of deciduous upper and lower second molars and the deciduous upper first molar are useful for diagnosing hominin taxa-especially Homo neanderthalensis and Homo sapiens. Building on these studies, we use geometric morphometric methods to assess the taxonomic significance of the crown outline of the lower first deciduous molar (dm1). We test whether the crown shape of the dm1 distinguishes H. neanderthalensis from H. sapiens and explore whether dm1 crown shape can be used to accurately assign individuals to taxa. Our fossil sample includes 3 early H. sapiens, 7 Upper Paleolithic H. sapiens, and 13 H. neanderthalensis individuals. Our recent human sample includes 103 individuals from Africa, Australia, Europe, South America, and South Asia. Our results indicate that H. neanderthalensis dm1s cluster fairly tightly and separate well from those of Upper Paleolithic H. sapiens. However, we also found that the range of shapes in the recent human sample completely overlaps the ranges of all fossil samples. Consequently, results of the quadratic discriminant analysis based on the first 8 principal components (PCs) representing more than 90% of the variation were mixed. Lower dm1s were correctly classified in 87.3% of the individuals; the combined H. sapiens sample had greater success (90.2%) in assigning individuals than did the H. neanderthalensis sample (61.5%). When the analysis was run removing the highly variable recent human sample, accuracy increased to 84.6% for H. neanderthalensis, and 57.1% of Upper Paleolithic H. sapiens were classified correctly by using the first 4 PCs (70.3%). We conclude that caution is warranted when assigning isolated dm1 crowns to taxa; while an assignment to H. neanderthalensis has a high probability of being correct, assignment to Upper Paleolithic H. sapiens is less certain.}, }
@article {pmid32918796, year = {2021}, author = {Breyl, M}, title = {Triangulating Neanderthal cognition: A tale of not seeing the forest for the trees.}, journal = {Wiley interdisciplinary reviews. Cognitive science}, volume = {12}, number = {2}, pages = {e1545}, doi = {10.1002/wcs.1545}, pmid = {32918796}, issn = {1939-5086}, mesh = {Animals ; *Biological Evolution ; *Cognition ; Humans ; *Language ; *Neanderthals ; }, abstract = {The inference of Neanderthal cognition, including their cultural and linguistic capabilities, has persisted as a fiercely debated research topic for decades. This lack of consensus is substantially based on inherent uncertainties in reconstructing prehistory out of indirect evidence as well as other methodological limitations. Further factors include systemic difficulties within interdisciplinary discourse, data artifacts, historic research biases, and the sheer scope of the relevant research. Given the degrees of freedom in interpretation ensuing from these complications, any attempt to find approximate answers to the yet unsettled pertinent discourse may not rest on single studies, but instead a careful and comprehensive interdisciplinary synthesis of findings. Triangulating Neanderthals' cognition by considering the plethora of data, diverse perspectives and aforementioned complexities present within the literature constitutes the currently most reliable pathway to tentative conclusions. While some uncertainties remain, such an approach paints the picture of an extensive shared humanity between anatomically modern humans and Neanderthals. This article is categorized under: Cognitive Biology > Evolutionary Roots of Cognition Linguistics > Evolution of Language.}, }
@article {pmid32914870, year = {2021}, author = {Oxilia, G and Bortolini, E and Badino, F and Bernardini, F and Gazzoni, V and Lugli, F and Romandini, M and Radini, A and Terlato, G and Marciani, G and Silvestrini, S and Menghi Sartorio, JC and Thun Hohenstein, U and Fiorenza, L and Kullmer, O and Tuniz, C and Moggi Cecchi, J and Talamo, S and Fontana, F and Peresani, M and Benazzi, S and Cristiani, E}, title = {Exploring late Paleolithic and Mesolithic diet in the Eastern Alpine region of Italy through multiple proxies.}, journal = {American journal of physical anthropology}, volume = {174}, number = {2}, pages = {232-253}, pmid = {32914870}, issn = {1096-8644}, mesh = {Animals ; Carbon Isotopes/analysis ; Dental Calculus/chemistry ; Diet/*history ; Feeding Behavior/*physiology ; History, Ancient ; Humans ; Italy ; Molar/pathology ; Neanderthals ; Paleontology ; Tooth Wear/pathology ; }, abstract = {OBJECTIVES: The analysis of prehistoric human dietary habits is key for understanding the effects of paleoenvironmental changes on the evolution of cultural and social human behaviors. In this study, we compare results from zooarchaeological, stable isotope and dental calculus analyses as well as lower second molar macrowear patterns to gain a broader understanding of the diet of three individuals who lived between the end of the Late Pleistocene and the Early Holocene (ca., 17-8 ky cal BP) in the Eastern Alpine region of Italy.<br><br>MATERIALS AND METHODS: We analyze individuals buried at the sites of Riparo Tagliente (Verona), Riparo Villabruna, and Mondeval de Sora (Belluno). The three burials provide a unique dataset for diachronically exploring the influence of climatic changes on human subsistence strategies.<br><br>RESULTS: Isotopic results indicate that all individuals likely relied on both terrestrial and freshwater animal proteins. Even though dental calculus analysis was, in part, hindered by the amount of mineral deposit available on the teeth, tooth macrowear study suggests that the dietary habits of the individuals included plant foods. Moreover, differences in macrowear patterns of lower second molars have been documented between Neanderthals and modern humans in the present sample, due to a prevalence of Buccal wear among the former as opposed to higher values of Lingual wear in modern human teeth.<br><br>DISCUSSION: Isotopic analyses have emphasized the contribution of animal proteins in the diet of the three foragers from the Eastern Alpine region. The possible intake of carbohydrate-rich plant foods, suggested by the retrieval of plant remains in dental calculus, is supported by the signal of macrowear analysis. Moreover, the latter method indicates that the distribution of macrowear in lower second molars (M2 s) allows us to discriminate between Neanderthals and modern humans within the present reference sample. Overall, our results show these three prehistoric hunter-gatherers were well adapted to the environment in which they lived exploiting many natural resources.}, }
@article {pmid32901061, year = {2020}, author = {Picin, A and Hajdinjak, M and Nowaczewska, W and Benazzi, S and Urbanowski, M and Marciszak, A and Fewlass, H and Bosch, MD and Socha, P and Stefaniak, K and Żarski, M and Wiśniewski, A and Hublin, JJ and Nadachowski, A and Talamo, S}, title = {New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14778}, pmid = {32901061}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; *Caves ; DNA, Mitochondrial/*analysis/genetics ; *Fossils ; Humans ; Neanderthals/classification/*genetics ; Phylogeny ; Poland ; Radiometric Dating ; Sequence Analysis, DNA ; Tooth/*anatomy &amp; histology/physiology ; }, abstract = {The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here, we present new data from the archaeological record of Stajnia Cave (Poland) and the paleogenetic analysis of a Neanderthal molar S5000, found in a Micoquian context. Our results demonstrate that the mtDNA genome of Stajnia S5000 dates to MIS 5a making the tooth the oldest Neanderthal specimen from Central-Eastern Europe. Furthermore, S5000 mtDNA has the fewest number of differences to mtDNA of Mezmaiskaya 1 Neanderthal from Northern Caucasus, and is more distant from almost contemporaneous Neanderthals of Scladina and Hohlenstein-Stadel. This observation and the technological affinity between Poland and the Northern Caucasus could be the result of increased mobility of Neanderthals that changed their subsistence strategy for coping with the new low biomass environments and the increased foraging radius of gregarious animals. The Prut and Dniester rivers were probably used as the main corridors of dispersal. The persistence of the Micoquian techno-complex in South-Eastern Europe infers that this axis of mobility was also used at the beginning of MIS 3 when a Neanderthal population turnover occurred in the Northern Caucasus.}, }
@article {pmid32889336, year = {2020}, author = {Romandini, M and Oxilia, G and Bortolini, E and Peyrégne, S and Delpiano, D and Nava, A and Panetta, D and Di Domenico, G and Martini, P and Arrighi, S and Badino, F and Figus, C and Lugli, F and Marciani, G and Silvestrini, S and Menghi Sartorio, JC and Terlato, G and Hublin, JJ and Meyer, M and Bondioli, L and Higham, T and Slon, V and Peresani, M and Benazzi, S}, title = {A late Neanderthal tooth from northeastern Italy.}, journal = {Journal of human evolution}, volume = {147}, number = {}, pages = {102867}, doi = {10.1016/j.jhevol.2020.102867}, pmid = {32889336}, issn = {1095-8606}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Cuspid/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Italy ; Maxilla ; Neanderthals/*anatomy &amp; histology ; Paleodontology ; Tooth, Deciduous/*anatomy &amp; histology ; }, abstract = {The site of Riparo Broion (Vicenza, northeastern Italy) preserves a stratigraphic sequence documenting the Middle-to-Upper Paleolithic transition, in particular the final Mousterian and the Uluzzian cultures. In 2018, a human tooth was retrieved from a late Mousterian level, representing the first human remain ever found from this rock shelter (Riparo Broion 1). Here, we provide the morphological description and taxonomic assessment of Riparo Broion 1 with the support of classic and virtual morphology, 2D and 3D analysis of the topography of enamel thickness, and DNA analysis. The tooth is an exfoliated right upper deciduous canine, and its general morphology and enamel thickness distribution support attribution to a Neanderthal child. Correspondingly, the mitochondrial DNA sequence from Riparo Broion 1 falls within the known genetic variation of Late Pleistocene Neanderthals, in accordance with newly obtained radiocarbon dates that point to approximately 48 ka cal BP as the most likely minimum age for this specimen. The present work describes novel and direct evidence of the late Neanderthal occupation in northern Italy that preceded the marked cultural and technological shift documented by the Uluzzian layers in the archaeological sequence at Riparo Broion. Here, we provide a new full morphological, morphometric, and taxonomic analysis of Riparo Broion 1, in addition to generating the wider reference sample of Neanderthal and modern human upper deciduous canines. This research contributes to increasing the sample of fossil remains from Italy, as well as the number of currently available upper deciduous canines, which are presently poorly documented in the scientific literature.}, }
@article {pmid32874601, year = {2020}, author = {Amos, W}, title = {Signals interpreted as archaic introgression appear to be driven primarily by faster evolution in Africa.}, journal = {Royal Society open science}, volume = {7}, number = {7}, pages = {191900}, pmid = {32874601}, issn = {2054-5703}, abstract = {Non-African humans appear to carry a few per cent archaic DNA due to ancient inter-breeding. This modest legacy and its likely recent timing imply that most introgressed fragments will be rare and hence will occur mainly in the heterozygous state. I tested this prediction by calculating D statistics, a measure of legacy size, for pairs of humans where one of the pair was conditioned always to be either homozygous or heterozygous. Using coalescent simulations, I confirmed that conditioning the non-African to be heterozygous increased D, while conditioning the non-African to be homozygous reduced D to zero. Repeating with real data reveals the exact opposite pattern. In African-non-African comparisons, D is near-zero if the African individual is held homozygous. Conditioning one of two Africans to be either homozygous or heterozygous invariably generates large values of D, even when both individuals are drawn from the same population. Invariably, the African with more heterozygous sites (conditioned heterozygous > unconditioned > conditioned homozygous) appears less related to the archaic. By contrast, the same analysis applied to pairs of non-Africans always yields near-zero D, showing that conditioning does not create large D without an underlying signal to expose. Large D values in humans are therefore driven almost entirely by heterozygous sites in Africans acting to increase divergence from related taxa such as Neanderthals. In comparison with heterozygous Africans, individuals that lack African heterozygous sites, whether non-African or conditioned homozygous African, always appear more similar to archaic outgroups, a signal previously interpreted as evidence for introgression. I hope these analyses will encourage others to consider increased divergence as well as increased similarity to archaics as mechanisms capable of driving asymmetrical base-sharing.}, }
@article {pmid32859969, year = {2020}, author = {Yousefi, M and Heydari-Guran, S and Kafash, A and Ghasidian, E}, title = {Species distribution models advance our knowledge of the Neanderthals' paleoecology on the Iranian Plateau.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14248}, pmid = {32859969}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Asia, Western ; Demography/*trends ; Ecology/history ; Europe ; Fossils ; Goats ; History, Ancient ; Humans ; Iran ; Models, Statistical ; Neanderthals/*physiology ; Paleontology/methods ; Sheep ; }, abstract = {Neanderthals (Homo neanderthalensis) were distributed across a vast region from Europe to western and Central Asia. The Neanderthals' paleoecology and distribution has been extensively studied in Europe where the species originated. However, very little is known about their paleoecology in south-western Asia. Here, we employed species distribution modelling and 45 Middle Palaeolithic (c. 200,000-40,000 years BCE) sites location associated with fossil and/or lithic artefacts made by the Neanderthals to examine the expansion of the Neanderthals on the Iranian Plateau in south-western Asia. We estimated the niche overlap between Neanderthals and wild goat, wild sheep and Persian gazelle by modelling their past distribution using 200, 143 and 110 occurrence records respectively. The results show that Neanderthals had highest niche overlap with wild goat in the study area. This analysis revealed that the most suitable Neanderthals' habitats in south-western Asia were located in the Zagros Mountains stretches from north-western and western and some isolated patches in the central parts of the Iranian Plateau. The annual precipitation and maximum temperature of the warmest month were the most important predictor of the species' distribution. This finding shows that the southern edge of the Neanderthals distribution was limited by warm summer. Our results provide important information for future field investigations and excavations in the area.}, }
@article {pmid32853200, year = {2020}, author = {Mughal, MR and Koch, H and Huang, J and Chiaromonte, F and DeGiorgio, M}, title = {Learning the properties of adaptive regions with functional data analysis.}, journal = {PLoS genetics}, volume = {16}, number = {8}, pages = {e1008896}, pmid = {32853200}, issn = {1553-7404}, support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; F31 HG010574/HG/NHGRI NIH HHS/United States ; T32 GM102057/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA-Binding Proteins/genetics ; Genetic Variation ; Humans ; Membrane Transport Proteins ; *Models, Genetic ; *Mutation Rate ; Neanderthals/genetics ; Selection, Genetic ; Software ; Whites/*genetics ; }, abstract = {Identifying regions of positive selection in genomic data remains a challenge in population genetics. Most current approaches rely on comparing values of summary statistics calculated in windows. We present an approach termed SURFDAWave, which translates measures of genetic diversity calculated in genomic windows to functional data. By transforming our discrete data points to be outputs of continuous functions defined over genomic space, we are able to learn the features of these functions that signify selection. This enables us to confidently identify complex modes of natural selection, including adaptive introgression. We are also able to predict important selection parameters that are responsible for shaping the inferred selection events. By applying our model to human population-genomic data, we recapitulate previously identified regions of selective sweeps, such as OCA2 in Europeans, and predict that its beneficial mutation reached a frequency of 0.02 before it swept 1,802 generations ago, a time when humans were relatively new to Europe. In addition, we identify BNC2 in Europeans as a target of adaptive introgression, and predict that it harbors a beneficial mutation that arose in an archaic human population that split from modern humans within the hypothesized modern human-Neanderthal divergence range.}, }
@article {pmid32839541, year = {2020}, author = {Telis, N and Aguilar, R and Harris, K}, title = {Selection against archaic hominin genetic variation in regulatory regions.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {11}, pages = {1558-1566}, pmid = {32839541}, issn = {2397-334X}, support = {R35 GM133428/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Regulatory Sequences, Nucleic Acid ; Selection, Genetic ; }, abstract = {Traces of Neandertal and Denisovan DNA persist in the modern human gene pool, but have been systematically purged by natural selection from genes and other functionally important regions. This implies that many archaic alleles harmed the fitness of hybrid individuals, but the nature of this harm is poorly understood. Here, we show that enhancers contain less Neandertal and Denisovan variation than expected given the background selection they experience, suggesting that selection acted to purge these regions of archaic alleles that disrupted their gene regulatory functions. We infer that selection acted mainly on young archaic variation that arose in Neandertals or Denisovans shortly before their contact with humans; enhancers are not depleted of older variants found in both archaic species. Some types of enhancer appear to have tolerated introgression better than others; compared with tissue-specific enhancers, pleiotropic enhancers show stronger depletion of archaic single-nucleotide polymorphisms. To some extent, evolutionary constraint is predictive of introgression depletion, but certain tissues' enhancers are more depleted of Neandertal and Denisovan alleles than expected given their comparative tolerance to new mutations. Foetal brain and muscle are the tissues whose enhancers show the strongest depletion of archaic alleles, but only brain enhancers show evidence of unusually stringent purifying selection. We conclude that epistatic incompatibilities between human and archaic alleles are needed to explain the degree of archaic variant depletion from foetal muscle enhancers, perhaps due to divergent selection for higher muscle mass in archaic hominins compared with humans.}, }
@article {pmid32817536, year = {2020}, author = {Bard, E and Heaton, TJ and Talamo, S and Kromer, B and Reimer, RW and Reimer, PJ}, title = {Extended dilation of the radiocarbon time scale between 40,000 and 48,000 y BP and the overlap between Neanderthals and Homo sapiens.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {35}, pages = {21005-21007}, pmid = {32817536}, issn = {1091-6490}, mesh = {Animals ; Calibration/standards ; Fossils ; Humans ; Neanderthals ; Paleontology/*methods ; Radiometric Dating/*methods ; }, abstract = {The new radiocarbon calibration curve (IntCal20) allows us to calculate the gradient of the relationship between [14]C age and calendar age over the past 55 millennia before the present (55 ka BP). The new gradient curve exhibits a prolonged and prominent maximum between 48 and 40 ka BP during which the radiocarbon clock runs almost twice as fast as it should. This radiocarbon time dilation is due to the increase in the atmospheric [14]C/[12]C ratio caused by the [14]C production rise linked to the transition into the Laschamp geomagnetic excursion centered around 41 ka BP. The major maximum in the gradient from 48 to 40 ka BP is a new feature of the IntCal20 calibration curve, with far-reaching impacts for scientific communities, such as prehistory and paleoclimatology, relying on accurate ages in this time range. To illustrate, we consider the duration of the overlap between Neanderthals and Homo sapiens in Eurasia.}, }
@article {pmid32813722, year = {2020}, author = {Delpiano, D and Uthmeier, T}, title = {Techno-functional and 3D shape analysis applied for investigating the variability of backed tools in the Late Middle Paleolithic of Central Europe.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0236548}, pmid = {32813722}, issn = {1932-6203}, mesh = {Animals ; Archaeology/*instrumentation ; Artifacts ; Behavior Rating Scale ; Fossils/*diagnostic imaging ; Humans ; Neanderthals ; Paleontology/*instrumentation ; Technology/*instrumentation ; Tool Use Behavior/classification ; }, abstract = {In the Late Middle Paleolithic of Central Europe, two main cultural complexes have been distinguished: the Micoquian or Keilmessergruppe (KMG), and the Mousterian. Their differences mainly consist in the frequence of some retouched tools and the presence of bifacial technology. When these industries coexist, one element of discussion is the application of different concepts to manufacture tools with the same techno-functionality. This is particularly true for backed artifacts, such as Keilmesser (backed, asymmetrical bifacially-shaped knives) opposed to flake-tools equipped with a natural or knapped back. We conducted a techno-functional analysis of the backed tools from the G-Layer-Complex of Sesselfelsgrotte, one of the main Late Middle Paleolithic sequences in Central Europe, characterized by a combination of KMG and Mousterian aspects. In order to better understand the morpho-metrical data, 3D scans were used for recording technical features and performing semi-automatic geometric morphometrics. Results indicate that the techno-functional schemes of Keilmesser show a moderate variability and often overlap with the schemes of other typological groups. Within bifacial backed knives, a process of imitation of unifacial flake tools' functionaly was recognized particularly in the cutting edge manufacturing. Keilmesser proved to be the long-life, versatile version of backed flake-tools, also due to the recurrent valence as both tool and core. This is why Keilmesser represent an ideal strategic blank when a mobile and multi-functional tool is needed. Based on these data, it is assumed that the relationship between Mousterian and KMG is deeply rooted and the emergence of KMG aspects could be related to constrained situations characterizing the long cold stages of the Early Weichselian. A higher regional mobility caused by the comparably low predictability of resources characterized the subsistence tactics of Neanderthal groups especially at the borders of their overall distribution. For this reason, Keilmesser could have represented an ecological answer before possibly becoming a marker of cultural identity.}, }
@article {pmid32805525, year = {2020}, author = {Torres-Tamayo, N and Schlager, S and García-Martínez, D and Sanchis-Gimeno, JA and Nalla, S and Ogihara, N and Oishi, M and Martelli, S and Bastir, M}, title = {Three-dimensional geometric morphometrics of thorax-pelvis covariation and its potential for predicting the thorax morphology: A case study on Kebara 2 Neandertal.}, journal = {Journal of human evolution}, volume = {147}, number = {}, pages = {102854}, doi = {10.1016/j.jhevol.2020.102854}, pmid = {32805525}, issn = {1095-8606}, mesh = {Animals ; Anthropology, Physical ; Fossils/*anatomy &amp; histology ; Image Processing, Computer-Assisted ; Israel ; Male ; Neanderthals/*anatomy &amp; histology ; Pelvis/*anatomy &amp; histology ; Thorax/*anatomy &amp; histology ; Tomography, X-Ray Computed ; }, abstract = {The skeletal torso is a complex structure of outstanding importance in understanding human body shape evolution, but reconstruction usually entails an element of subjectivity as researchers apply their own anatomical expertise to the process. Among different fossil reconstruction methods, 3D geometric morphometric techniques have been increasingly used in the last decades. Two-block partial least squares analysis has shown great potential for predicting missing elements by exploiting the covariation between two structures (blocks) in a reference sample: one block can be predicted from the other one based on the strength of covariation between blocks. The first aim of this study is to test whether this predictive approach can be used for predicting thorax morphologies from pelvis morphologies within adult Homo sapiens reference samples with known covariation between the thorax and the pelvis. The second aim is to apply this method to Kebara 2 Neandertal (Israel, ∼60 ka) to predict its thorax morphology using two different pelvis reconstructions as predictors. We measured 134 true landmarks, 720 curve semilandmarks, and 160 surface semilandmarks on 60 3D virtual torso models segmented from CT scans. We conducted three two-block partial least squares analyses between the thorax (block 1) and the pelvis (block 2) based on the H. sapiens reference samples after performing generalized Procrustes superimposition on each block separately. Comparisons of these predictions in full shape space by means of Procrustes distances show that the male-only predictive model yields the most reliable predictions within modern humans. In addition, Kebara 2 thorax predictions based on this model concur with the thorax morphology proposed for Neandertals. The method presented here does not aim to replace other techniques, but to rather complement them through quantitative prediction of a virtual 'scaffold' to articulate the thoracic fossil elements, thus extending the potential of missing data estimation beyond the methods proposed in previous works.}, }
@article {pmid32760067, year = {2020}, author = {Hubisz, MJ and Williams, AL and Siepel, A}, title = {Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph.}, journal = {PLoS genetics}, volume = {16}, number = {8}, pages = {e1008895}, pmid = {32760067}, issn = {1553-7404}, support = {R35 GM127070/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Evolution, Molecular ; *Gene Flow ; Human Migration ; Humans ; *Models, Genetic ; Neanderthals/*genetics ; Population/*genetics ; *Recombination, Genetic ; }, abstract = {The sequencing of Neanderthal and Denisovan genomes has yielded many new insights about interbreeding events between extinct hominins and the ancestors of modern humans. While much attention has been paid to the relatively recent gene flow from Neanderthals and Denisovans into modern humans, other instances of introgression leave more subtle genomic evidence and have received less attention. Here, we present a major extension of the ARGweaver algorithm, called ARGweaver-D, which can infer local genetic relationships under a user-defined demographic model that includes population splits and migration events. This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topologies and branch lengths along the genome, but also indicate migrant lineages. The sampled ARGs can therefore be parsed to produce probabilities of introgression along the genome. We show that this method is well powered to detect the archaic migration into modern humans, even with only a few samples. We then show that the method can also detect introgressed regions stemming from older migration events, or from unsampled populations. We apply it to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. Finally, we predict that 1% of the Denisovan genome was introgressed from an unsequenced, but highly diverged, archaic hominin ancestor. About 15% of these "super-archaic" regions-comprising at least about 4Mb-were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.}, }
@article {pmid32750315, year = {2020}, author = {Course, MM and Gudsnuk, K and Smukowski, SN and Winston, K and Desai, N and Ross, JP and Sulovari, A and Bourassa, CV and Spiegelman, D and Couthouis, J and Yu, CE and Tsuang, DW and Jayadev, S and Kay, MA and Gitler, AD and Dupre, N and Eichler, EE and Dion, PA and Rouleau, GA and Valdmanis, PN}, title = {Evolution of a Human-Specific Tandem Repeat Associated with ALS.}, journal = {American journal of human genetics}, volume = {107}, number = {3}, pages = {445-460}, pmid = {32750315}, issn = {1537-6605}, support = {T32 GM007454/GM/NIGMS NIH HHS/United States ; U24 AG041689/AG/NIA NIH HHS/United States ; R01 DK078424/DK/NIDDK NIH HHS/United States ; P30 AG066509/AG/NIA NIH HHS/United States ; P50 AG005136/AG/NIA NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptor Proteins, Signal Transducing/*genetics ; Aged ; Alzheimer Disease/genetics/pathology ; Amyotrophic Lateral Sclerosis/*genetics/pathology ; DNA Repeat Expansion/genetics ; *Evolution, Molecular ; Female ; Gene Expression Regulation/genetics ; Humans ; Male ; Minisatellite Repeats/genetics ; Phenotype ; Species Specificity ; Tandem Repeat Sequences/*genetics ; }, abstract = {Tandem repeats are proposed to contribute to human-specific traits, and more than 40 tandem repeat expansions are known to cause neurological disease. Here, we characterize a human-specific 69 bp variable number tandem repeat (VNTR) in the last intron of WDR7, which exhibits striking variability in both copy number and nucleotide composition, as revealed by long-read sequencing. In addition, greater repeat copy number is significantly enriched in three independent cohorts of individuals with sporadic amyotrophic lateral sclerosis (ALS). Each unit of the repeat forms a stem-loop structure with the potential to produce microRNAs, and the repeat RNA can aggregate when expressed in cells. We leveraged its remarkable sequence variability to align the repeat in 288 samples and uncover its mechanism of expansion. We found that the repeat expands in the 3'-5' direction, in groups of repeat units divisible by two. The expansion patterns we observed were consistent with duplication events, and a replication error called template switching. We also observed that the VNTR is expanded in both Denisovan and Neanderthal genomes but is fixed at one copy or fewer in non-human primates. Evaluating the repeat in 1000 Genomes Project samples reveals that some repeat segments are solely present or absent in certain geographic populations. The large size of the repeat unit in this VNTR, along with our multiplexed sequencing strategy, provides an unprecedented opportunity to study mechanisms of repeat expansion, and a framework for evaluating the roles of VNTRs in human evolution and disease.}, }
@article {pmid32745133, year = {2020}, author = {Örd, T and Puurand, T and Örd, D and Annilo, T and Möls, M and Remm, M and Örd, T}, title = {A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals.}, journal = {PLoS genetics}, volume = {16}, number = {8}, pages = {e1008981}, pmid = {32745133}, issn = {1553-7404}, support = {HHSN268201000029C/HL/NHLBI NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; }, mesh = {Cell Cycle Proteins/*genetics ; Estonia/epidemiology ; Female ; Gene Expression Regulation/genetics ; *Genetic Heterogeneity ; *Genetics, Population ; Genotype ; Humans ; Male ; Minisatellite Repeats/*genetics ; Promoter Regions, Genetic ; Protein Serine-Threonine Kinases/*antagonists &amp; inhibitors/genetics ; RNA-Seq ; Repressor Proteins/*genetics ; Whole Genome Sequencing ; }, abstract = {Tribbles homolog 3 (TRIB3) is pseudokinase involved in intracellular regulatory processes and has been implicated in several diseases. In this article, we report that human TRIB3 promoter contains a 33-bp variable number tandem repeat (VNTR) and characterize the heterogeneity and function of this genetic element. Analysis of human populations around the world uncovered the existence of alleles ranging from 1 to 5 copies of the repeat, with 2-, 3- and 5-copy alleles being the most common but displaying considerable geographical differences in frequency. The repeated sequence overlaps a C/EBP-ATF transcriptional regulatory element and is highly conserved, but not repeated, in various mammalian species, including great apes. The repeat is however evident in Neanderthal and Denisovan genomes. Reporter plasmid experiments in human cell culture reveal that an increased copy number of the TRIB3 promoter 33-bp repeat results in increased transcriptional activity. In line with this, analysis of whole genome sequencing and RNA-Seq data from human cohorts demonstrates that the copy number of TRIB3 promoter 33-bp repeats is positively correlated with TRIB3 mRNA expression level in many tissues throughout the body. Moreover, the copy number of the TRIB3 33-bp repeat appears to be linked to known TRIB3 eQTL SNPs as well as TRIB3 SNPs reported in genetic association studies. Taken together, the results indicate that the promoter 33-bp VNTR constitutes a causal variant for TRIB3 expression variation between individuals and could underlie the results of SNP-based genetic studies.}, }
@article {pmid32735718, year = {2020}, author = {Ríos, L and Cardoso, HFV}, title = {Comment on 'Krapina atlases suggest a high prevalence of anatomical variations in the first cervical vertebra of Neanderthals'.}, journal = {Journal of anatomy}, volume = {237}, number = {6}, pages = {1185-1188}, pmid = {32735718}, issn = {1469-7580}, mesh = {*Neanderthals ; Prevalence ; Spine ; }, abstract = {A review of the observation of an anterior cleft on the atlas of a Neanderthal from Krapina.}, }
@article {pmid32732402, year = {2020}, author = {Gibbons, A}, title = {How an ancient microbial arms race remodeled human cells.}, journal = {Science (New York, N.Y.)}, volume = {369}, number = {6503}, pages = {491-492}, doi = {10.1126/science.369.6503.491}, pmid = {32732402}, issn = {1095-9203}, mesh = {Animals ; Cell Membrane/chemistry/microbiology ; Communicable Diseases/*genetics ; *Evolution, Molecular ; Host-Pathogen Interactions/*genetics ; Humans ; Immune System/*cytology ; N-Acetylneuraminic Acid/metabolism ; Neanderthals/*genetics/*microbiology ; Selection, Genetic ; }, }
@article {pmid32721654, year = {2020}, author = {Grine, FE and Mongle, CS and Smith, SL and Black, W and du Plessis, A and Braga, J}, title = {Human manual distal phalanges from the Middle Stone Age deposits of Klasies River Main Site, Western Cape Province, South Africa.}, journal = {Journal of human evolution}, volume = {146}, number = {}, pages = {102849}, doi = {10.1016/j.jhevol.2020.102849}, pmid = {32721654}, issn = {1095-8606}, mesh = {Caves ; Finger Phalanges/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Humans ; South Africa ; }, abstract = {Two new distal manual phalanges from the Middle Stone Age deposits of Klasies River Main Site are described. One (SAM-AP 6387) likely derives from ray II or ray III, whereas the other (SAM-AP 6388) is from the thumb. Both derive from a late adolescent or fully adult individual. They were recovered by H. Deacon from the same stratigraphic unit (submember W or possibly submember R) of the Shell and Sand Member of Cave 1, which places them between 100 and 90 ka. Both are comparatively small elements, and the possibility that they came from the same hand cannot be discounted at this time. These bones add to the meager and all too fragmentary postcranial human fossil sample from the Late Pleistocene of South Africa. These two specimens provide some additional evidence pertaining to the morphological attributes of the distal phalanges of the Middle Stone Age inhabitants of South Africa. Together with the distal pollical phalanx from Die Kelders (SAM-AP 6402), they are relatively small in comparison with homologs from recent human samples as well as Late Pleistocene specimens from Eurasia. Given their small sizes, the distal pollical phalanges from Klasies and Die Kelders are not dissimilar to Holocene Khoesan homologs. As expected, the Klasies elements differ noticeably from Neandertal homologs, especially in the narrowness of their shafts and distal tuberosities.}, }
@article {pmid32719451, year = {2020}, author = {Rinker, DC and Simonti, CN and McArthur, E and Shaw, D and Hodges, E and Capra, JA}, title = {Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {10}, pages = {1332-1341}, pmid = {32719451}, issn = {2397-334X}, support = {K22 CA184308/CA/NCI NIH HHS/United States ; T32 GM080178/GM/NIGMS NIH HHS/United States ; T32 EY021453/EY/NEI NIH HHS/United States ; F30 HG011200/HG/NHGRI NIH HHS/United States ; R01 GM115836/GM/NIGMS NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Haplotypes ; *Hominidae ; Humans ; *Neanderthals/genetics ; Population ; }, abstract = {Neanderthal ancestry remains across modern Eurasian genomes and introgressed sequences influence diverse phenotypes. Here, we demonstrate that introgressed sequences reintroduced thousands of ancestral alleles that were lost in Eurasian populations before introgression. Our simulations and variant effect predictions argue that these reintroduced alleles (RAs) are more likely to be tolerated by modern humans than are introgressed Neanderthal-derived alleles (NDAs) due to their distinct evolutionary histories. Consistent with this, we show enrichment for RAs and depletion for NDAs on introgressed haplotypes with expression quantitative trait loci (eQTL) and phenotype associations. Analysis of available cross-population eQTLs and massively parallel reporter assay data show that RAs commonly influence gene expression independent of linked NDAs. We further validate these independent effects for one RA in vitro. Finally, we demonstrate that NDAs are depleted for regulatory activity compared to RAs, while RAs have activity levels similar to non-introgressed variants. In summary, our study reveals that Neanderthal introgression reintroduced thousands of lost ancestral variants with gene regulatory activity and that these RAs were more tolerated than NDAs. Thus, RAs and their distinct evolutionary histories must be considered when evaluating the effects of introgression.}, }
@article {pmid32717667, year = {2020}, author = {Sankararaman, S}, title = {Methods for detecting introgressed archaic sequences.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {85-90}, pmid = {32717667}, issn = {1879-0380}, support = {R35 GM125055/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA/analysis/*genetics ; *Evolution, Molecular ; Genetic Variation ; *Genome, Human ; Hominidae/*genetics ; Humans ; *Models, Genetic ; Neanderthals/*genetics ; }, abstract = {Analysis of genome sequences from archaic and modern humans have revealed multiple episodes of admixture between highly-diverged population groups. Statistical methods that attempt to localize DNA segments introduced by these events offer a powerful tool to investigate recent human evolution. We review recent advances in methods for detecting introgressed sequences.}, }
@article {pmid32707058, year = {2020}, author = {Zeberg, H and Dannemann, M and Sahlholm, K and Tsuo, K and Maricic, T and Wiebe, V and Hevers, W and Robinson, HPC and Kelso, J and Pääbo, S}, title = {A Neanderthal Sodium Channel Increases Pain Sensitivity in Present-Day Humans.}, journal = {Current biology : CB}, volume = {30}, number = {17}, pages = {3465-3469.e4}, doi = {10.1016/j.cub.2020.06.045}, pmid = {32707058}, issn = {1879-0445}, mesh = {Adult ; Aged ; Amino Acid Substitution ; Animals ; Female ; Humans ; Male ; Middle Aged ; *Mutation ; NAV1.7 Voltage-Gated Sodium Channel/genetics/*metabolism ; Neanderthals ; Pain/genetics/metabolism/*pathology ; Xenopus laevis ; }, abstract = {The sodium channel Nav1.7 is crucial for impulse generation and conduction in peripheral pain pathways [1]. In Neanderthals, the Nav1.7 protein carried three amino acid substitutions (M932L, V991L, and D1908G) relative to modern humans. We expressed Nav1.7 proteins carrying all combinations of these substitutions and studied their electrophysiological effects. Whereas the single amino acid substitutions do not affect the function of the ion channel, the full Neanderthal variant carrying all three substitutions, as well as the combination of V991L with D1908G, shows reduced inactivation, suggesting that peripheral nerves were more sensitive to painful stimuli in Neanderthals than in modern humans. We show that, due to gene flow from Neanderthals, the three Neanderthal substitutions are found in ∼0.4% of present-day Britons, where they are associated with heightened pain sensitivity.}, }
@article {pmid32704108, year = {2020}, author = {Callaway, E}, title = {Neanderthal gene linked to increased pain sensitivity.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {32704108}, issn = {1476-4687}, }
@article {pmid32699254, year = {2020}, author = {Sánchez-Romero, L and Benito-Calvo, A and Marín-Arroyo, AB and Agudo-Pérez, L and Karampaglidis, T and Rios-Garaizar, J}, title = {Author Correction: New insights for understanding spatial patterning and formation processes of the Neanderthal occupation in the Amalda I cave (Gipuzkoa, Spain).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12456}, doi = {10.1038/s41598-020-68761-1}, pmid = {32699254}, issn = {2045-2322}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32697783, year = {2020}, author = {Baumann, C and Bocherens, H and Drucker, DG and Conard, NJ}, title = {Fox dietary ecology as a tracer of human impact on Pleistocene ecosystems.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0235692}, pmid = {32697783}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; Bayes Theorem ; Bone and Bones/metabolism ; Carbon Isotopes/analysis ; Collagen/chemistry/metabolism ; Diet/*veterinary ; *Ecosystem ; Fossils/history ; Foxes/*physiology ; History, Ancient ; Humans ; Neanderthals ; Nitrogen Isotopes/analysis ; }, abstract = {Nowadays, opportunistic small predators, such as foxes (Vulpes vulpes and Vulpes lagopus), are well known to be very adaptable to human modified ecosystems. However, the timing of the start of this phenomenon in terms of human impact on ecosystems and of the implications for foxes has hardly been studied. We hypothesize that foxes can be used as an indicator of past human impact on ecosystems, as a reflection of population densities and consequently to track back the influence of humans on the Pleistocene environment. To test this hypothesis, we used stable isotope analysis (δ13C, δ15N) of bone collagen extracted from faunal remains from several archaeological sites located in the Swabian Jura (southwest Germany) and covering a time range over three important cultural periods, namely the Middle Palaeolithic (older than 42,000 years ago) attributed to Neanderthals, and the early Upper Palaeolithic periods Aurignacian and Gravettian (42,000 to 30,000 years ago) attributed to modern humans. We then ran Bayesian statistic systems (SIBER, mixSIAR) to reconstruct the trophic niches and diets of Pleistocene foxes. We observed that during the Middle Palaeolithic period, when Neanderthals sparsely populated the Swabian Jura, the niches occupied by foxes suggest a natural trophic behavior. In contrast, during the early Upper Palaeolithic periods, a new trophic fox niche appeared, characterized by a restricted diet on reindeer. This trophic niche could be due to the consumption of human subsidies related to a higher human population density and the resulting higher impact on the Pleistocene environment by modern humans compared to Neanderthals. Furthermore, our study suggests that, a synanthropic commensal behavior of foxes started already in the Aurignacian, around 42,000 years ago.}, }
@article {pmid32696095, year = {2020}, author = {Peeters, S and Zwart, H}, title = {Neanderthals as familiar strangers and the human spark: How the 'golden years' of Neanderthal research reopen the question of human uniqueness.}, journal = {History and philosophy of the life sciences}, volume = {42}, number = {3}, pages = {33}, pmid = {32696095}, issn = {1742-6316}, mesh = {Animals ; *Biological Evolution ; Humans ; Neanderthals/*psychology ; }, abstract = {During the past decades, our image of Homo neanderthalensis has changed dramatically. Initially, Neanderthals were seen as primitive brutes. Increasingly, however, Neanderthals are regarded as basically human. New discoveries and technologies have led to an avalanche of data, and as a result of that it becomes increasingly difficult to pinpoint what the difference between modern humans and Neanderthals really is. And yet, the persistent quest for a minimal difference which separates them from us is still noticeable in Neanderthal research. Neanderthal discourse is a vantage point from which the logic of 'us' versus 'other' is critically reconsidered. Studying contemporary academic literature and science autobiographies from an oblique perspective, focusing not on Neanderthals as objects, but on the dynamics of interaction between Neanderthal researchers and their finds, basic convictions at work in this type of research are retrieved. What is at issue is not the actual distinction between modern humans and Neanderthals (which is continuously being redefined), but rather the dualistic construction of human and nonhuman. Neanderthal understanding is affected by the desire to safeguard human uniqueness. The overall trend is to identify the human mark or spark, which defines us as favoured 'winners'. The paradoxes emerging in contemporary Neanderthal discourse are symptomatic of the fact that a dualistic style of thinking is no longer tenable.}, }
@article {pmid32690317, year = {2020}, author = {Montinaro, F and Capelli, C}, title = {A Worldwide Map of Human Structural Variants.}, journal = {Trends in genetics : TIG}, volume = {36}, number = {10}, pages = {722-725}, doi = {10.1016/j.tig.2020.07.002}, pmid = {32690317}, issn = {0168-9525}, mesh = {Genomics ; Humans ; *Neanderthals/genetics ; }, abstract = {Genomic variation extends from single nucleotide variants to large chromosomal rearrangements, but the extent of structural variation in Homo sapiens is still unclear. Almarri et al. provide a worldwide catalogue of structural variants present in human populations. Most of the reported variation is novel, with some variants being inherited from Neanderthals and Denisovans. Drift and selection shaped the distribution of these variants with some suggested to have functional implications.}, }
@article {pmid32681013, year = {2020}, author = {Marra, F and Rolfo, MF and Gaeta, M and Florindo, F}, title = {Anomalous Last Interglacial Tyrrhenian sea levels and Neanderthal settling at Guattari and Moscerini caves (central Italy).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11929}, pmid = {32681013}, issn = {2045-2322}, abstract = {We present a geological-stratigraphical study aimed to provide chronologic constraints to the sea-level markers occurring at two coastal caves of central Italy (Grotta Guattari and Grotta dei Moscerini) and to the Neanderthal frequentation of these caves, in the light of recent archaeological and geomorphological-geochronological studies suggesting similar sea levels during MIS 5.5 and MIS 5.3, and only few m below the Present during MIS 5.1 in this region. Based on the review of previous literature data, combined with new stratigraphic observations at Grotta Guattari and re-analysis of archive material including unpublished field notes from Grotta dei Moscerini, we reconstruct a plausible sea-level history accounting for the lithological and paleoenvironmental features of their sedimentary fillings. In particular, we outline the abundant occurrence of well-rounded pumice clasts within the sedimentary deposits of Moscerini Cave, attesting for the proximity to the beach where this pumice was gathered by wave action. Through the petrographic and geochemical analysis of this pumice we evidence provenance from Phlegraean Fields and Ischia Island volcanic districts, framing their chronology in the time span 118-40 ka, consistent with literature ESR-U/Th dates providing ages ranging 101 ± 5-74 ± 7 ka for the sedimentary filling of both Moscerini and Guattari caves.}, }
@article {pmid32673890, year = {2020}, author = {Hérisson, D and Soriano, S}, title = {A view of the Lower to Middle Paleolithic boundary from Northern France, far from the Near East?.}, journal = {Journal of human evolution}, volume = {145}, number = {}, pages = {102814}, doi = {10.1016/j.jhevol.2020.102814}, pmid = {32673890}, issn = {1095-8606}, mesh = {*Animal Migration ; Animals ; Archaeology ; *Cultural Evolution ; Fossils ; France ; Geologic Sediments/*analysis ; *Human Migration ; Humans ; Middle East ; Neanderthals ; *Tool Use Behavior ; }, abstract = {Northern France and the Near East play and have played a central role in the debate around the Lower Paleolithic (LP) to Middle Paleolithic (MP) boundary. In the early 1990s, the renewed Saalian record for Northern France began to outline a mosaic model of the LP-to-MP transition-mainly based on Tuffreau's works. It implied the coexistence of Upper Acheulean assemblages (numerous bifaces with few standardized retouched flakes), 'Epi-Acheulean' assemblages (rare bifaces and diversified retouched flakes), and Mousterian assemblages (Levalloisian industries) during the Marine Isotope Stage (MIS) 8-6 period. Since the 2000s, the discovery of new key sites and enhanced field and laboratory methods are challenging this model. We present first a brief historical summary of previous approaches to the LP to MP boundary in Northern France. A large data set of Saalian archaeological units available from previous works has been updated and expanded to include additional sites. This allows us to demonstrate that the current Saalian record from Northern France is both rich and sparse as it is heterogeneously biased through time and space and that these biases limit the accuracy of any attempt to model the LP-to-MP transition. Nevertheless, we describe the differences between pre-MIS 9 and MIS 9 and MIS 8-6 records for lithic industries and discuss whether the current periodization is still relevant considering new data on technological, behavioral, and cultural changes. The comparison between Northern France and Near Eastern records allows regional cultural patterns to be distinguished from global trends in lithic trajectories of change and determination of how they slotted together. Our review of the available data from these two distant regions confirms that the LP-to-MP transition is probably one of the major cultural shifts in human evolution.}, }
@article {pmid32666166, year = {2021}, author = {Hallast, P and Agdzhoyan, A and Balanovsky, O and Xue, Y and Tyler-Smith, C}, title = {A Southeast Asian origin for present-day non-African human Y chromosomes.}, journal = {Human genetics}, volume = {140}, number = {2}, pages = {299-307}, pmid = {32666166}, issn = {1432-1203}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa ; Asians/*genetics ; Chromosomes, Human, Y/*genetics ; DNA/genetics ; Emigration and Immigration ; Genetics, Population/methods ; Genome, Human/genetics ; Haplotypes/genetics ; Humans ; Male ; Phylogeny ; Phylogeography/methods ; }, abstract = {The genomes of present-day humans outside Africa originated almost entirely from a single out-migration ~ 50,000-70,000 years ago, followed by mixture with Neanderthals contributing ~ 2% to all non-Africans. However, the details of this initial migration remain poorly understood because no ancient DNA analyses are available from this key time period, and interpretation of present-day autosomal data is complicated due to subsequent population movements/reshaping. One locus, however, does retain male-specific information from this early period: the Y chromosome, where a detailed calibrated phylogeny has been constructed. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations. Here, we show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y chromosomes, all point to East/Southeast Asia as the origin 50,000-55,000 years ago of all known surviving non-African male lineages (apart from recent migrants). This observation contrasts with the expectation of a West Eurasian origin predicted by a simple model of expansion from a source near Africa, and can be interpreted as resulting from extensive genetic drift in the initial population or replacement of early western Y lineages from the east, thus informing and constraining models of the initial expansion.}, }
@article {pmid32661407, year = {2020}, author = {Columbu, A and Chiarini, V and Spötl, C and Benazzi, S and Hellstrom, J and Cheng, H and De Waele, J}, title = {Author Correction: Speleothem record attests to stable environmental conditions during Neanderthal-modern human turnover in southern Italy.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {9}, pages = {1279}, doi = {10.1038/s41559-020-1267-6}, pmid = {32661407}, issn = {2397-334X}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32659509, year = {2020}, author = {Kuzmin, YV and Keates, SG}, title = {The chronology of hominin fossils from the Altai Mountains, Siberia: An alternative view.}, journal = {Journal of human evolution}, volume = {146}, number = {}, pages = {102834}, doi = {10.1016/j.jhevol.2020.102834}, pmid = {32659509}, issn = {1095-8606}, mesh = {Animals ; Caves ; *Fossils/anatomy &amp; histology ; *Hominidae/anatomy &amp; histology ; Humans ; Neanderthals/anatomy &amp; histology ; Siberia ; }, }
@article {pmid32652819, year = {2020}, author = {Pomeroy, E and Hunt, CO and Reynolds, T and Abdulmutalb, D and Asouti, E and Bennett, P and Bosch, M and Burke, A and Farr, L and Foley, R and French, C and Frumkin, A and Goldberg, P and Hill, E and Kabukcu, C and Lahr, MM and Lane, R and Marean, C and Maureille, B and Mutri, G and Miller, CE and Mustafa, KA and Nymark, A and Pettitt, P and Sala, N and Sandgathe, D and Stringer, C and Tilby, E and Barker, G}, title = {Issues of theory and method in the analysis of Paleolithic mortuary behavior: A view from Shanidar Cave.}, journal = {Evolutionary anthropology}, volume = {29}, number = {5}, pages = {263-279}, doi = {10.1002/evan.21854}, pmid = {32652819}, issn = {1520-6505}, mesh = {Animals ; Burial/*history ; Caves ; Fossils ; Fractures, Bone/pathology ; Geologic Sediments/chemistry ; History, Ancient ; Iraq ; Neanderthals/*physiology ; *Paleontology ; }, abstract = {Mortuary behavior (activities concerning dead conspecifics) is one of many traits that were previously widely considered to have been uniquely human, but on which perspectives have changed markedly in recent years. Theoretical approaches to hominin mortuary activity and its evolution have undergone major revision, and advances in diverse archeological and paleoanthropological methods have brought new ways of identifying behaviors such as intentional burial. Despite these advances, debates concerning the nature of hominin mortuary activity, particularly among the Neanderthals, rely heavily on the rereading of old excavations as new finds are relatively rare, limiting the extent to which such debates can benefit from advances in the field. The recent discovery of in situ articulated Neanderthal remains at Shanidar Cave offers a rare opportunity to take full advantage of these methodological and theoretical developments to understand Neanderthal mortuary activity, making a review of these advances relevant and timely.}, }
@article {pmid32632262, year = {2020}, author = {Columbu, A and Chiarini, V and Spötl, C and Benazzi, S and Hellstrom, J and Cheng, H and De Waele, J}, title = {Speleothem record attests to stable environmental conditions during Neanderthal-modern human turnover in southern Italy.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {9}, pages = {1188-1195}, pmid = {32632262}, issn = {2397-334X}, mesh = {Europe ; Humans ; Italy ; *Neanderthals ; }, abstract = {The causes of Neanderthal-modern human (MH) turnover are ambiguous. While potential biocultural interactions between the two groups are still little known, it is clear that Neanderthals in southern Europe disappeared about 42 thousand years ago (ka) after cohabitation for ~3,000 years with MH. Among a plethora of hypotheses on Neanderthal extinction, rapid climate changes during the Middle to Upper Palaeolithic transition (MUPT) are regarded as a primary factor. Here we show evidence for stable climatic and environmental conditions during the MUPT in a region (Apulia) where Neanderthals and MH coexisted. We base our findings on a rare glacial stalagmite deposited between ~106 and ~27 ka, providing the first continuous western Mediterranean speleothem palaeoclimate archive for this period. The uninterrupted growth of the stalagmite attests to the constant availability of rainfall and vegetated soils, while its δ[13]C-δ[18]O palaeoclimate proxies demonstrate that Apulia was not affected by dramatic climate oscillations during the MUPT. Our results imply that, because climate did not play a key role in the disappearance of Neanderthals in this area, Neanderthal-MH turnover must be approached from a perspective that takes into account climatic and environmental conditions favourable for both species.}, }
@article {pmid32632258, year = {2020}, author = {Bastir, M and García-Martínez, D and Torres-Tamayo, N and Palancar, CA and Beyer, B and Barash, A and Villa, C and Sanchis-Gimeno, JA and Riesco-López, A and Nalla, S and Torres-Sánchez, I and García-Río, F and Been, E and Gómez-Olivencia, A and Haeusler, M and Williams, SA and Spoor, F}, title = {Rib cage anatomy in Homo erectus suggests a recent evolutionary origin of modern human body shape.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {9}, pages = {1178-1187}, pmid = {32632258}, issn = {2397-334X}, mesh = {Adolescent ; Adult ; Animals ; Biological Evolution ; *Hominidae ; Human Body ; Humans ; *Neanderthals ; *Rib Cage ; }, abstract = {The tall and narrow body shape of anatomically modern humans (Homo sapiens) evolved via changes in the thorax, pelvis and limbs. It is debated, however, whether these modifications first evolved together in African Homo erectus, or whether H. erectus had a more primitive body shape that was distinct from both the more ape-like Australopithecus species and H. sapiens. Here we present the first quantitative three-dimensional reconstruction of the thorax of the juvenile H. erectus skeleton, KNM-WT 15000, from Nariokotome, Kenya, along with its estimated adult rib cage, for comparison with H. sapiens and the Kebara 2 Neanderthal. Our three-dimensional reconstruction demonstrates a short, mediolaterally wide and anteroposteriorly deep thorax in KNM-WT 15000 that differs considerably from the much shallower thorax of H. sapiens, pointing to a recent evolutionary origin of fully modern human body shape. The large respiratory capacity of KNM-WT 15000 is compatible with the relatively stocky, more primitive, body shape of H. erectus.}, }
@article {pmid32615344, year = {2020}, author = {Yan, SM and McCoy, RC}, title = {Archaic hominin genomics provides a window into gene expression evolution.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {44-49}, pmid = {32615344}, issn = {1879-0380}, support = {R35 GM133747/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical ; DNA/analysis/*genetics ; *Evolution, Molecular ; Fossils ; *Gene Expression Regulation ; *Genetic Variation ; Genomics/*methods ; Hominidae ; Humans ; Neanderthals ; }, abstract = {Differences in gene expression are thought to account for most phenotypic differences within and between species. Consequently, gene expression is a powerful lens through which to study divergence between modern humans and our closest evolutionary relatives, the Neanderthals and Denisovans. Such insights complement biological knowledge gleaned from the fossil record, while also revealing general features of the mode and tempo of regulatory evolution. Because of the degradation of ancient RNA, gene expression profiles of archaic hominins must be studied by indirect means. As such, conclusions drawn from these studies are often laden with assumptions about the genetic architecture of gene expression, the complexity of which is increasingly apparent. Despite these challenges, rapid technical and conceptual advances in the fields of ancient genomics, functional genomics, statistical genomics, and genome engineering are revolutionizing understanding of hominin gene expression evolution.}, }
@article {pmid32612423, year = {2020}, author = {Senturk, N and Ergoren, MC}, title = {Developing an Online Portal for Determining the Genomic Signature of Archaic DNA that are Associated to Modern Human Genetic Diseases: A Meta-Analysis Study.}, journal = {The Eurasian journal of medicine}, volume = {52}, number = {2}, pages = {153-160}, pmid = {32612423}, issn = {1308-8734}, abstract = {OBJECTIVE: Mutations or introgression can cause and rise adaptive alleles of which some can be beneficial. Archaic humans lived more than 200,000 years ago in Europe and Western Asia. They were adapted to the environment and pathogens that prevailed in these locations. It can therefore be thought that modern humans obtained significant immune advantage from the archaic alleles.<br><br>MATERIALS AND METHODS: First, data were collected by meta-analysis from previously identified genetic diseases caused by alleles that were introgressed from archaics. Second, the in silico model portal (http://www.archaics2phenotype.xxx.edu.tr) was designed to trace the history of the Neanderthal allele. The portal also shows the current distribution of the genotypes of the selected alleles within different populations and correlates with the individuals phenotype.<br><br>RESULTS: Our developed model provides a better understanding for the origin of genetic diseases or traits that are associated with the Neanderthal genome.<br><br>CONCLUSION: The developed medicine model will help individuals and their populations to receive the best treatment. It also clarifies why there are differences in disease phenotypes in modern humans.}, }
@article {pmid32594872, year = {2020}, author = {Nielsen, M and Langley, MC and Shipton, C and Kapitány, R}, title = {Homo neanderthalensis and the evolutionary origins of ritual in Homo sapiens.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1805}, pages = {20190424}, pmid = {32594872}, issn = {1471-2970}, mesh = {Animals ; Archaeology ; *Ceremonial Behavior ; *Cultural Evolution ; Neanderthals/*psychology ; }, abstract = {There is a large, if disparate, body of archaeological literature discussing specific instantiations of symbolic material culture and the possibility of ritual practices in Neanderthal populations. Despite this attention, however, no single synthesis exists that draws upon cognitive, psychological and cultural evolutionary theories of ritual. Here, we review the evidence for ritual-practice among now-extinct Homo neanderthalensis, as well as the necessary cognitive pre-conditions for such behaviour, in order to explore the evolution of ritual in Homo sapiens. We suggest that the currently available archaeological evidence indicates that Neanderthals may have used 'ritualization' to increase the successful transmission of technical knowledge across generations-providing an explanation for the technological stability of the Middle Palaeolithic and attesting to a survival strategy differing from near-contemporary H. sapiens. This article is part of the theme issue 'Ritual renaissance: new insights into the most human of behaviours'.}, }
@article {pmid32593870, year = {2020}, author = {Martínez de Pinillos, M and Martín-Francés, L and de Castro, JMB and García-Campos, C and Modesto-Mata, M and Martinón-Torres, M and Vialet, A}, title = {Inner morphological and metric characterization of the molar remains from the Montmaurin-La Niche mandible: The Neanderthal signal.}, journal = {Journal of human evolution}, volume = {145}, number = {}, pages = {102739}, doi = {10.1016/j.jhevol.2019.102739}, pmid = {32593870}, issn = {1095-8606}, mesh = {*Animal Migration ; Animals ; Biological Evolution ; Dentin/*anatomy &amp; histology ; Europe ; Fossils/anatomy &amp; histology ; Mandible/*anatomy &amp; histology ; Molar/*anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Paleontology ; X-Ray Microtomography ; }, abstract = {Here, we present a metric and morphological study of the molar remains from the Montmaurin-La Niche mandible by means of microcomputed tomography. According to the last analysis, based on the combination of geomorphological and paleontological data, the level bearing this human mandible probably corresponds to the marine isotope stages (MIS) 7. These data place the Montmaurin-La Niche in a chronologically intermediate position between the Neanderthals and the Middle Pleistocene fossils (e.g., Sima de los Huesos, la Caune de l'Arago). A recent study has revealed that while the mandible is more closely related to the Early and Middle Pleistocene African and Eurasian populations, the morphology of the outer enamel surfaces of its molars is typical of the Neanderthal linage. The data presented here are in line with this finding because the morphology of the enamel-dentine junction of the molars is similar to that of Neanderthals, whereas the absolute and relative enamel thickness values (2D and 3D) are closer to those exhibited by some Early Pleistocene hominins. Moreover, the pulp cavity morphology and proportions are in concordance with the Neanderthal populations. Our results strengthen the hypothesis that the settlement of Europe could be the result of several migrations, at different times, originated from a common source population. Thus, the variability in the European Middle Pleistocene populations (e.g., Montmaurin, Sima de los Huesos, Arago, Mala Balanica) could indicate different migrations at different times and/or population fragmentation, without excluding the possible hybridization between residents and new settlers.}, }
@article {pmid32586278, year = {2020}, author = {Weiß, CL and Gansauge, MT and Aximu-Petri, A and Meyer, M and Burbano, HA}, title = {Mining ancient microbiomes using selective enrichment of damaged DNA molecules.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {432}, pmid = {32586278}, issn = {1471-2164}, mesh = {Animals ; Bacteria/*classification/genetics ; DNA, Ancient/*analysis/chemistry ; DNA, Bacterial/genetics ; Data Mining ; Fossils/*microbiology ; Gene Library ; Metagenomics ; Microbiota ; Neanderthals/microbiology ; Plants/microbiology ; Sequence Analysis, DNA/*methods ; Uracil/*chemistry ; }, abstract = {BACKGROUND: The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Here, we employ a library preparation method that separates molecules that carry uracils from those that do not for a set of samples that includes Neandertal remains, herbarium specimens and archaeological plant remains.<br><br>RESULTS: We show that sequencing DNA libraries enriched in molecules carrying uracils effectively amplifies age associated degradation patterns in microbial mixtures of ancient and historical origin. This facilitates the discovery of authentic ancient microbial taxa in cases where degradation patterns are difficult to detect due to large sequence divergence in microbial mixtures. Additionally, the relative enrichment of taxa in the uracil enriched fraction can help to identify bona fide ancient microbial taxa that could be missed using a more targeted approach.<br><br>CONCLUSIONS: Our experiments show, that in addition to its use in enriching authentic endogenous DNA of organisms of interest, the selective enrichment of damaged DNA molecules can be a valuable tool in the discovery of ancient microbial taxa.}, }
@article {pmid32580077, year = {2020}, author = {Bosman, AM and Reyes-Centeno, H and Harvati, K}, title = {A virtual assessment of the suprainiac depressions on the Eyasi I (Tanzania) and Aduma ADU-VP-1/3 (Ethiopia) Pleistocene hominin crania.}, journal = {Journal of human evolution}, volume = {145}, number = {}, pages = {102815}, doi = {10.1016/j.jhevol.2020.102815}, pmid = {32580077}, issn = {1095-8606}, mesh = {Animals ; Anthropology, Physical ; Biological Evolution ; Ethiopia ; Fossils/*anatomy &amp; histology ; Humans ; Neanderthals/*anatomy &amp; histology ; Occipital Bone/*anatomy &amp; histology ; Principal Component Analysis ; Tanzania ; Tomography, X-Ray Computed ; }, abstract = {Despite a steady increase in our understanding of the phenotypic variation of Pleistocene Homo, debate continues over phylogenetically informative features. One such trait is the suprainiac fossa, a depression on the occipital bone above inion that is commonly considered an autapomorphy of the Neanderthal lineage. Challenging this convention, depressions in the suprainiac region have also been described for two Pleistocene hominin crania from sub-Saharan Africa: Eyasi I (Tanzania) and ADU-VP-1/3 (Ethiopia). Here, we use a combined quantitative and qualitative approach, using μCT imaging, to investigate the occipital depressions on these specimens. The results show that neither the external nor the internal morphologies of these depressions bear any resemblance to the Neanderthal condition. A principal component analysis based on multiple thickness measurements along the occipital squama demonstrates that the relative thickness values for the internal structures in Eyasi I and ADU-VP-1/3 are within the range of Homo sapiens. Thus, our results support the autapomorphic status of the Neanderthal suprainiac fossa and highlight the need to use nuanced approaches and multiple lines of evidence.}, }
@article {pmid32574964, year = {2020}, author = {Mathov, Y and Batyrev, D and Meshorer, E and Carmel, L}, title = {Harnessing epigenetics to study human evolution.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {23-29}, doi = {10.1016/j.gde.2020.05.023}, pmid = {32574964}, issn = {1879-0380}, mesh = {*DNA Methylation ; *Epigenesis, Genetic ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Human ; Humans ; }, abstract = {Recent advances in ancient DNA extraction and high-throughput sequencing technologies enabled the high-quality sequencing of archaic genomes, including the Neanderthal and the Denisovan. While comparisons with modern humans revealed both archaic-specific and human-specific sequence changes, in the absence of gene expression information, understanding the functional implications of such genetic variations remains a major challenge. To study gene regulation in archaic humans, epigenetic research comes to our aid. DNA methylation, which is highly correlated with transcription, can be directly measured in modern samples, as well as reconstructed in ancient samples. This puts DNA methylation as a natural basis for comparative epigenetics between modern humans, archaic humans and nonhuman primates.}, }
@article {pmid32559457, year = {2020}, author = {Dannemann, M and He, Z and Heide, C and Vernot, B and Sidow, L and Kanton, S and Weigert, A and Treutlein, B and Pääbo, S and Kelso, J and Camp, JG}, title = {Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions.}, journal = {Stem cell reports}, volume = {15}, number = {1}, pages = {214-225}, pmid = {32559457}, issn = {2213-6711}, mesh = {Alleles ; Animals ; Brain/metabolism ; Cell Line ; DNA/*genetics ; Haplotypes/genetics ; Humans ; Neanderthals/*genetics ; Phenotype ; Pluripotent Stem Cells/cytology ; RNA/metabolism ; Stem Cells/cytology/*metabolism ; }, abstract = {Induced pluripotent stem cells (iPSCs) from diverse humans offer the potential to study human functional variation in controlled culture environments. A portion of this variation originates from an ancient admixture between modern humans and Neandertals, which introduced alleles that left a phenotypic legacy on individual humans today. Here, we show that a large iPSC repository harbors extensive Neandertal DNA, including alleles that contribute to human phenotypes and diseases, encode hundreds of amino acid changes, and alter gene expression in specific tissues. We provide a database of the inferred introgressed Neandertal alleles for each individual iPSC line, together with the annotation of the predicted functional variants. We also show that transcriptomic data from organoids generated from iPSCs can be used to track Neandertal-derived RNA over developmental processes. Human iPSC resources provide an opportunity to experimentally explore Neandertal DNA function and its contribution to present-day phenotypes, and potentially study Neandertal traits.}, }
@article {pmid32556248, year = {2020}, author = {Khan, N and de Manuel, M and Peyregne, S and Do, R and Prufer, K and Marques-Bonet, T and Varki, N and Gagneux, P and Varki, A}, title = {Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins.}, journal = {Genome biology and evolution}, volume = {12}, number = {7}, pages = {1040-1050}, pmid = {32556248}, issn = {1759-6653}, support = {R01 GM032373/GM/NIGMS NIH HHS/United States ; U01 MH106874/MH/NIMH NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Gene Expression ; Genome ; Hominidae/*genetics/immunology ; Humans ; Immunity, Innate/genetics ; Multigene Family ; Mutation ; Polymorphism, Genetic ; Selection, Genetic ; Sialic Acid Binding Ig-like Lectin 3/*genetics ; }, abstract = {Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface "self-associated molecular patterns" that modulate innate immunity via engagement of CD33-related-Siglec receptors. The Alu-fusion-mediated loss-of-function of CMAH fixed ∼2-3 Ma, possibly contributing to the origins of the genus Homo. The mutation likely altered human self-associated molecular patterns, triggering multiple events, including emergence of human-adapted pathogens with strong preference for Neu5Ac recognition and/or presenting Neu5Ac-containing molecular mimics of human glycans, which can suppress immune responses via CD33-related-Siglec engagement. Human-specific alterations reported in some gene-encoding Sia-sensing proteins suggested a "hotspot" in hominin evolution. The availability of more hominid genomes including those of two extinct hominins now allows full reanalysis and evolutionary timing. Functional changes occur in 8/13 members of the human genomic cluster encoding CD33-related Siglecs, all predating the human common ancestor. Comparisons with great ape genomes indicate that these changes are unique to hominins. We found no evidence for strong selection after the Human-Neanderthal/Denisovan common ancestor, and these extinct hominin genomes include almost all major changes found in humans, indicating that these changes in hominin sialobiology predate the Neanderthal-human divergence ∼0.6 Ma. Multiple changes in this genomic cluster may also explain human-specific expression of CD33rSiglecs in unexpected locations such as amnion, placental trophoblast, pancreatic islets, ovarian fibroblasts, microglia, Natural Killer(NK) cells, and epithelia. Taken together, our data suggest that innate immune interactions with pathogens markedly altered hominin Siglec biology between 0.6 and 2 Ma, potentially affecting human evolution.}, }
@article {pmid32546518, year = {2020}, author = {Mafessoni, F and Grote, S and de Filippo, C and Slon, V and Kolobova, KA and Viola, B and Markin, SV and Chintalapati, M and Peyrégne, S and Skov, L and Skoglund, P and Krivoshapkin, AI and Derevianko, AP and Meyer, M and Kelso, J and Peter, B and Prüfer, K and Pääbo, S}, title = {A high-coverage Neandertal genome from Chagyrskaya Cave.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {26}, pages = {15132-15136}, pmid = {32546518}, issn = {1091-6490}, mesh = {Animals ; Biological Evolution ; Female ; Fossils ; Gene Expression Regulation ; Genetic Variation ; *Genome ; Humans ; Inbreeding ; Neanderthals/*genetics ; Population Density ; Russia ; }, abstract = {We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to Neandertals in western Eurasia [Prüfer et al., Science 358, 655-658 (2017); Hajdinjak et al., Nature 555, 652-656 (2018)] than to Neandertals who lived earlier in Denisova Cave [Prüfer et al., Nature 505, 43-49 (2014)], which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with the fact that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino-acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.}, }
@article {pmid32531199, year = {2020}, author = {Almarri, MA and Bergström, A and Prado-Martinez, J and Yang, F and Fu, B and Dunham, AS and Chen, Y and Hurles, ME and Tyler-Smith, C and Xue, Y}, title = {Population Structure, Stratification, and Introgression of Human Structural Variation.}, journal = {Cell}, volume = {182}, number = {1}, pages = {189-199.e15}, pmid = {32531199}, issn = {1097-4172}, support = {/WT_/Wellcome Trust/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; FC001595/MRC_/Medical Research Council/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Alleles ; Databases, Genetic ; Gene Dosage ; Gene Duplication ; Gene Frequency/genetics ; Genetic Variation ; *Genetics, Population ; Genome, Human ; *Genomic Structural Variation ; Humans ; }, abstract = {Structural variants contribute substantially to genetic diversity and are important evolutionarily and medically, but they are still understudied. Here we present a comprehensive analysis of structural variation in the Human Genome Diversity panel, a high-coverage dataset of 911 samples from 54 diverse worldwide populations. We identify, in total, 126,018 variants, 78% of which were not identified in previous global sequencing projects. Some reach high frequency and are private to continental groups or even individual populations, including regionally restricted runaway duplications and putatively introgressed variants from archaic hominins. By de novo assembly of 25 genomes using linked-read sequencing, we discover 1,643 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence absent from the GRCh38 reference. Our results illustrate the limitation of a single human reference and the need for high-quality genomes from diverse populations to fully discover and understand human genetic variation.}, }
@article {pmid32511250, year = {2020}, author = {Martín-Francés, L and Martinón-Torres, M and Martínez de Pinillos, M and García-Campos, C and Zanolli, C and Bayle, P and Modesto-Mata, M and Arsuaga, JL and Bermúdez de Castro, JM}, title = {Crown tissue proportions and enamel thickness distribution in the Middle Pleistocene hominin molars from Sima de los Huesos (SH) population (Atapuerca, Spain).}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0233281}, pmid = {32511250}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Dental Enamel/anatomy &amp; histology/metabolism ; Fossils/*anatomy &amp; histology ; Hominidae/*anatomy &amp; histology ; Humans ; Molar/*anatomy &amp; histology/metabolism ; Neanderthals ; Phylogeny ; Spain ; Tooth ; Tooth Crown/anatomy &amp; histology/metabolism ; }, abstract = {Dental enamel thickness, topography, growth and development vary among hominins. In Homo, the thickness of dental enamel in most Pleistocene hominins display variations from thick to hyper-thick, while Neanderthals exhibit proportionally thinner enamel. The origin of the thin trait remains unclear. In this context, the Middle Pleistocene human dental assemblage from Atapuerca-Sima de los Huesos (SH) provides a unique opportunity to trace the evolution of enamel thickness in European hominins. In this study, we aim to test the hypothesis if the SH molar sample approximates the Neanderthal condition for enamel thickness and/or distribution. This study includes 626 molars, both original and comparative data. We analysed the molar inner structural organization of the original collections (n = 124), belonging to SH(n = 72) and modern humans from Spanish origin (n = 52). We compared the SH estimates to those of extinct and extant populations of the genus Homo from African, Asian and European origin (estimates extracted from literature n = 502). The comparative sample included maxillary and mandibular molars belonging to H. erectus, East and North African Homo, European Middle Pleistocene Homo, Neanderthals, and fossil and extant H. sapiens. We used high-resolution images to investigate the endostructural configuration of SH molars (tissue proportions, enamel thickness and distribution). The SH molars exhibit on average thick absolute and relative enamel in 2D and 3D estimates, both in the complete crown and the lateral enamel. This primitive condition is shared with the majority of extinct and extant hominin sample, except for Neanderthals and some isolated specimens. On the contrary, the SH molar enamel distribution maps reveal a distribution pattern similar to the Neanderthal signal (with thicker enamel on the lingual cusps and more peripherally distributed), compared to H. antecessor and modern humans. Due to the phylogenetic position of the SH population, the thick condition in molars could represent the persistence of the plesiomorphic condition in this group. Still, more data is needed on other Early and Middle Pleistocene populations to fully understand the evolutionary meaning of this trait.}, }
@article {pmid32494067, year = {2020}, author = {Skov, L and Coll Macià, M and Sveinbjörnsson, G and Mafessoni, F and Lucotte, EA and Einarsdóttir, MS and Jonsson, H and Halldorsson, B and Gudbjartsson, DF and Helgason, A and Schierup, MH and Stefansson, K}, title = {The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes.}, journal = {Nature}, volume = {582}, number = {7810}, pages = {78-83}, pmid = {32494067}, issn = {1476-4687}, mesh = {Animals ; Female ; Genetic Association Studies ; Genetic Introgression/*genetics ; Genome, Human/*genetics ; *Genomics ; Haploidy ; Humans ; Iceland ; Male ; *Mutation ; Neanderthals/*genetics ; Phenotype ; Phylogeny ; }, abstract = {Human evolutionary history is rich with the interbreeding of divergent populations. Most humans outside of Africa trace about 2% of their genomes to admixture from Neanderthals, which occurred 50-60 thousand years ago[1]. Here we examine the effect of this event using 14.4 million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566 Icelanders, corresponding to a range of 56,388-112,709 unique archaic fragments that cover 38.0-48.2% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5% of fragments to an Altai or Vindija Neanderthal origin and 3.3% to Denisovan origin; 12.2% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans. A within-individual, paired comparison of archaic fragments with syntenic non-archaic fragments revealed that, although the overall rate of mutation was similar in humans and Neanderthals during the 500 thousand years that their lineages were separate, there were differences in the relative frequencies of mutation types-perhaps due to different generation intervals for males and females. Finally, we assessed 271 phenotypes, report 5 associations driven by variants in archaic fragments and show that the majority of previously reported associations are better explained by non-archaic variants.}, }
@article {pmid32490227, year = {2020}, author = {Kolendrianou, M and Ligkovanlis, S and Maniakas, I and Tzortzi, M and Iliopoulos, G}, title = {The Palaeolithic cave of Kalamakia (Mani Peninsula), Greece: new insights on the palaeoenvironment using microvertebrates and mesowear analysis of ruminant teeth.}, journal = {Heliyon}, volume = {6}, number = {5}, pages = {e03958}, pmid = {32490227}, issn = {2405-8440}, abstract = {In the present study, results from the examination of mammalian teeth from the cave of Kalamakia with modern techniques, as well as a qualitative overview of the microvertebrate and lithic material, are presented together with a revision of previous related work done for the site, in order to assess the palaeoenvironmental conditions in the area and the role they played in the Neanderthal's repeated occupation of the cave. Geometric morphometrics analyses performed on the first lower molars of Microtus spp. individuals revealed persistent populations of the subgenus Terricola, in which the presence of Microtus thomasi and Microtus subterraneus are continuous through the stratigraphic units. Mesowear analyses performed on ruminant teeth showed no significant variation in toothwear through time, except for relatively elevated levels of dietary abrasion for the more recent samples. The study of the lithics revealed that Neanderthals visited the cave in alternating short and more permanent episodes of occupation, with the human occupants exhibiting special concern for raw material economy, while exploiting poor raw materials for the construction of their tools. The overview of the microvertebrate remains showed a growing trend towards the upper stratigraphic units, where taxa typical of temperate climate, open woodland and shrubland become more dominant. These results, along with observations derived from previous studies, suggest that temperate climate and open environment were the factors that mainly contributed to making the cave of Kalamakia attractive as a habitation site to the humans of the area.}, }
@article {pmid32470872, year = {2020}, author = {Key, AJM and Farr, I and Hunter, R and Winter, SL}, title = {Muscle recruitment and stone tool use ergonomics across three million years of Palaeolithic technological transitions.}, journal = {Journal of human evolution}, volume = {144}, number = {}, pages = {102796}, doi = {10.1016/j.jhevol.2020.102796}, pmid = {32470872}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; *Biological Evolution ; Electromyography ; *Ergonomics ; Forearm ; Hand ; *Hominidae ; Humans ; Muscle, Skeletal/*physiology ; Neanderthals ; Shoulder ; *Technology ; *Tool Use Behavior ; }, abstract = {Ergonomic relationships that minimize muscle activity relative to the creation of cutting stress underpin the design of modern knives, saws, and axes. The Palaeolithic archaeological record, and the > 3 million years of technological behavior that it represents, is predominantly characterized by sharp stone implements used for cutting. To date, we do not know whether Palaeolithic hominins adhered to ergonomic principles when designing stone tools, if lithic technological transitions were linked to ease-of-use advances, or even how muscularly demanding different Palaeolithic tools are on an empirically defined relative basis. Here, we report the results of an experimental program that examines how four key stone tool types, produced between ∼ 3.3 million and ∼ 40 thousand years ago, influence muscle activation in the hominin upper limb. Using standardized laboratory-based tests designed to imitate Pleistocene cutting behaviors, surface electromyography recorded electrical activity (amplitude) in nine muscles across the hand, forearm and shoulder of modern humans during the use of replica Lomekwian, Oldowan, Acheulean and Mousterian stone tools. Results confirm digit flexors and abductors, particularly the first dorsal interosseous and flexor pollicis longus, to be the most heavily recruited muscles during the use of all tool types. Significant differences in muscle activation are, however, identified dependent on the type of stone tool used. Notably, the abductor digiti minimi, flexor pollicis longus, and biceps brachii were highly activated during handaxe use, particularly when compared to the use of Oldowan and Levallois flakes. Results are discussed in light of current understanding on the origin of Lower and Middle Palaeolithic technologies, why specific tool types were produced over others during these periods, and the extent to which early hominins produced ergonomically designed tools.}, }
@article {pmid32457436, year = {2020}, author = {Sánchez-Romero, L and Benito-Calvo, A and Marín-Arroyo, AB and Agudo-Pérez, L and Karampaglidis, T and Rios-Garaizar, J}, title = {New insights for understanding spatial patterning and formation processes of the Neanderthal occupation in theAmalda I cave (Gipuzkoa, Spain).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8733}, pmid = {32457436}, issn = {2045-2322}, abstract = {The Level VII of Amalda I cave (Gipuzkoa, Spain) represents one of the latest Middle Palaeolithic occupations in the Cantabrian Region. It is characterized by the presence of Middle Palaeolithic lithic industry and animal remains, with clear evidences of anthropic and carnivore manipulation. At this site, the Neanderthal presence has been questioned in relation to the role of carnivores in the accumulation of large, medium-sized and small mammals. It has also been proposed that the Neanderthal occupation could have consisted of short-term occupations, where different activities took place in a structured space within the cave. However, all hypotheses lacked any integrative analysis of the site formation processes. With the aim of understanding these processes, a combination of spatial techniques, based on GIS and inferential statistics (density analysis, hotspots tools and palaeotopographic reconstruction), along with the taphonomic study of identifiable and non-identifiable macromammals remains, were employed. This study has revealed distinct use of the cave space by Neanderthals and carnivores. The major concentrations of lithics and medium-size mammal remains were clearly accumulated by humans at the cave entrance, while the small-size mammals were gathered by carnivores in an inner zone. The activities of the Neanderthals seem to be distinctly structured, suggesting a parallel exploitation of resources.}, }
@article {pmid32453742, year = {2020}, author = {Natri, HM and Bobowik, KS and Kusuma, P and Crenna Darusallam, C and Jacobs, GS and Hudjashov, G and Lansing, JS and Sudoyo, H and Banovich, NE and Cox, MP and Gallego Romero, I}, title = {Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago.}, journal = {PLoS genetics}, volume = {16}, number = {5}, pages = {e1008749}, pmid = {32453742}, issn = {1553-7404}, mesh = {CpG Islands ; *DNA Methylation ; Environment ; Epigenesis, Genetic/physiology ; Ethnicity/*genetics/statistics &amp; numerical data ; Gene Expression Profiling/statistics &amp; numerical data ; *Gene-Environment Interaction ; Genetics, Population ; Genome-Wide Association Study/statistics &amp; numerical data ; Genomics/methods ; Humans ; Indonesia/epidemiology ; Islands/epidemiology ; Pacific Islands/epidemiology ; Pedigree ; Phenotype ; Polymorphism, Single Nucleotide ; RNA-Seq ; *Transcriptome ; }, abstract = {Indonesia is the world's fourth most populous country, host to striking levels of human diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10.55% of tested genes are differentially expressed between the islands of Sumba and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.80% of genes correlating with nearby promoter CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia's tropical role as a source of infectious disease diversity and the strong selective pressures these diseases have exerted on humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by fine-scale environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes.}, }
@article {pmid32451437, year = {2020}, author = {Esteller-Cucala, P and Maceda, I and Børglum, AD and Demontis, D and Faraone, SV and Cormand, B and Lao, O}, title = {Genomic analysis of the natural history of attention-deficit/hyperactivity disorder using Neanderthal and ancient Homo sapiens samples.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8622}, pmid = {32451437}, issn = {2045-2322}, mesh = {Alleles ; Animals ; Attention Deficit Disorder with Hyperactivity/*genetics/history/pathology ; Bayes Theorem ; Databases, Genetic ; Deep Learning ; Evolution, Molecular ; *Genome, Human ; Genomics/*methods ; History, Ancient ; Humans ; Neanderthals/*genetics ; }, abstract = {Attention-deficit/hyperactivity disorder (ADHD) is an impairing neurodevelopmental condition highly prevalent in current populations. Several hypotheses have been proposed to explain this paradox, mainly in the context of the Paleolithic versus Neolithic cultural shift but especially within the framework of the mismatch theory. This theory elaborates on how a particular trait once favoured in an ancient environment might become maladaptive upon environmental changes. However, given the lack of genomic data available for ADHD, these theories have not been empirically tested. We took advantage of the largest GWAS meta-analysis available for this disorder consisting of over 20,000 individuals diagnosed with ADHD and 35,000 controls, to assess the evolution of ADHD-associated alleles in European populations using archaic, ancient and modern human samples. We also included Approximate Bayesian computation coupled with deep learning analyses and singleton density scores to detect human adaptation. Our analyses indicate that ADHD-associated alleles are enriched in loss of function intolerant genes, supporting the role of selective pressures in this early-onset phenotype. Furthermore, we observed that the frequency of variants associated with ADHD has steadily decreased since Paleolithic times, particularly in Paleolithic European populations compared to samples from the Neolithic Fertile Crescent. We demonstrate this trend cannot be explained by African admixture nor Neanderthal introgression, since introgressed Neanderthal alleles are enriched in ADHD risk variants. All analyses performed support the presence of long-standing selective pressures acting against ADHD-associated alleles until recent times. Overall, our results are compatible with the mismatch theory for ADHD but suggest a much older time frame for the evolution of ADHD-associated alleles compared to previous hypotheses.}, }
@article {pmid32451090, year = {2020}, author = {Hoffmann, DL and Standish, CD and García-Diez, M and Pettitt, PB and Milton, JA and Zilhão, J and Alcolea-González, JJ and Cantalejo-Duarte, P and Collado, H and de Balbín, R and Lorblanchet, M and Ramos-Muñoz, J and Weniger, GC and Pike, AWG}, title = {Response to White et al.'s reply: 'Still no archaeological evidence that Neanderthals created Iberian cave art' [J. Hum. Evol. (2020) 102640].}, journal = {Journal of human evolution}, volume = {144}, number = {}, pages = {102810}, doi = {10.1016/j.jhevol.2020.102810}, pmid = {32451090}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Caves ; *Neanderthals ; }, }
@article {pmid32437543, year = {2020}, author = {Zeberg, H and Kelso, J and Pääbo, S}, title = {The Neandertal Progesterone Receptor.}, journal = {Molecular biology and evolution}, volume = {37}, number = {9}, pages = {2655-2660}, pmid = {32437543}, issn = {1537-1719}, mesh = {Alleles ; Alu Elements ; Animals ; Female ; Fertility/*genetics ; *Genetic Introgression ; Haplotypes ; Humans ; Neanderthals/*genetics ; Pregnancy ; Premature Birth/*genetics ; Receptors, Progesterone/*genetics ; }, abstract = {The hormone progesterone is important for preparing the uterine lining for egg implantation and for maintaining the early stages of pregnancy. The gene encoding the progesterone receptor (PGR) carries introgressed Neandertal haplotypes with two missense substitutions and a mobile Alu element. These Neandertal gene variants have reached nearly 20% frequency in non-Africans and have been associated with preterm birth. Here, we show that one of the missense substitutions appears fixed in Neandertals, while the other substitution as well as the Alu insertion were polymorphic among Neandertals. We show that two Neandertal haplotypes carrying the PGR gene entered the modern human population and that present-day carriers of the Neandertal haplotypes express higher levels of the receptor. In a cohort of present-day Britons, these carriers have more siblings, fewer miscarriages, and less bleeding during early pregnancy suggesting that the Neandertal progesterone receptor alleles promote fertility. This may explain their high frequency in modern human populations.}, }
@article {pmid32436615, year = {2020}, author = {Palancar, CA and García-Martínez, D and Radovčić, D and Llidó, S and Mata-Escolano, F and Bastir, M and Sanchis-Gimeno, JA}, title = {Krapina atlases suggest a high prevalence of anatomical variations in the first cervical vertebra of Neanderthals.}, journal = {Journal of anatomy}, volume = {237}, number = {3}, pages = {579-586}, pmid = {32436615}, issn = {1469-7580}, mesh = {Animals ; Biological Evolution ; Biological Variation, Individual ; Cervical Atlas/*anatomy &amp; histology ; Fossils ; Neanderthals/*anatomy &amp; histology ; }, abstract = {The first cervical vertebra, atlas, and its anatomical variants have been widely studied in Homo sapiens. However, in Neanderthals, the presence of anatomical variants of the atlas has been very little studied until very recently. Only the Neanderthal group from the El Sidrón site (Spain) has been analysed with regard to the anatomical variants of the atlas. A high prevalence of anatomical variants has been described in this sample, which points to low genetic diversity in this Neanderthal group. Even so, the high prevalence of anatomical variations detected in El Sidrón Neanderthal atlases needs to be confirmed by analysing more Neanderthal remains. In this context, we analysed the possible presence of anatomical variants in the three Neanderthal atlases recovered from the Krapina site (Croatia) within the Neanderthal lineage. Two of the three Krapina atlases presented anatomical variations. One atlas (Krapina 98) had an unclosed transverse foramen and the other (Krapina 99) presented a non-fused anterior atlas arch. Moreover, an extended review of the bibliography also showed these anatomical variations in other Middle and Upper Pleistocene hominins, leading us to hypothesise that anatomical variations of the atlas had a higher prevalence in extinct hominins than in modern humans.}, }
@article {pmid32436183, year = {2020}, author = {Ricci, C and Kakularam, KR and Marzocchi, C and Capecchi, G and Riolo, G and Boschin, F and Kuhn, H and Castagna, MG and Cantara, S}, title = {Thr92Ala polymorphism in the type 2 deiodinase gene: an evolutionary perspective.}, journal = {Journal of endocrinological investigation}, volume = {43}, number = {12}, pages = {1749-1757}, doi = {10.1007/s40618-020-01287-5}, pmid = {32436183}, issn = {1720-8386}, mesh = {Alanine/genetics ; Alleles ; Amino Acid Substitution/genetics ; Animals ; *Evolution, Molecular ; Gene Frequency ; Genetics, Population ; Geography ; History, Ancient ; Humans ; Iodide Peroxidase/*genetics ; Neanderthals/genetics ; *Polymorphism, Single Nucleotide ; Threonine/genetics ; }, abstract = {PURPOSE: In the past, a role of thyroid hormones in human evolution has been hypothesized. T3, the metabolically active form, derives from extrathyroidal conversion of T4 by deionidase 2 (D2) enzyme encoded by DIO2 gene. In thyroid-deficient patients, decreased levels of free T3 have been associated with the polymorphism rs225014 A/G in DIO2, which causes the substitution of Threonine with Alanine (p.Thr92Ala) at protein level.<br><br>METHODS: We compared DNA and protein sequences of D2 from archaic human subspecies with those of contemporary humans.<br><br>RESULTS: Neanderthals and Denisovans displayed only the G allele at the rs225014 polymorphism, which encodes for an Alanine on the amino acid level. These data suggest that these hominines were homozygous for the Ala amino acid. These arcaic humans often lived in condition of iodine deficiency and thus, defective mechanisms of T3 biosynthesis could be life threatining. A reduced D2 activity is likely to cause decreased T3 levels, which could be critical for those individuals. Neanderthals and Denisovans were hunters/gatherers, and their diet was mainly based on the consumption of meat, with a low intake of carbohydrates. The need for circulating T3 is reduced at such alimentary conditions. On the basis of our genome comparisons the A allele, corresponding to Threonine and associated with higher levels of circulating T3 in thyroid-deficient patients, appeared for the first time during evolution in Anatomically Modern Humans during the Upper Pleistocene and has been conserved during the Neolithic age. With the advent of agriculture and herding, individuals carrying A allele might have a higher probability for surviving and reproducing. Thus, the variant was positively selected during the evolution.<br><br>CONCLUSION: Here we present an evolutionary perspective for p.Thr92Ala variant of D2 from Neanderthals to Anatomically Modern Humans.}, }
@article {pmid32433609, year = {2020}, author = {Hublin, JJ and Sirakov, N and Aldeias, V and Bailey, S and Bard, E and Delvigne, V and Endarova, E and Fagault, Y and Fewlass, H and Hajdinjak, M and Kromer, B and Krumov, I and Marreiros, J and Martisius, NL and Paskulin, L and Sinet-Mathiot, V and Meyer, M and Pääbo, S and Popov, V and Rezek, Z and Sirakova, S and Skinner, MM and Smith, GM and Spasov, R and Talamo, S and Tuna, T and Wacker, L and Welker, F and Wilcke, A and Zahariev, N and McPherron, SP and Tsanova, T}, title = {Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria.}, journal = {Nature}, volume = {581}, number = {7808}, pages = {299-302}, pmid = {32433609}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; }, mesh = {Animals ; Asia ; Bone and Bones/metabolism ; Bulgaria ; Caves ; DNA, Ancient/isolation &amp; purification ; DNA, Mitochondrial/genetics/isolation &amp; purification ; Europe ; *Fossils ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals/genetics ; Phylogeny ; Tool Use Behavior ; Tooth/anatomy &amp; histology/metabolism ; }, abstract = {The Middle to Upper Palaeolithic transition in Europe witnessed the replacement and partial absorption of local Neanderthal populations by Homo sapiens populations of African origin[1]. However, this process probably varied across regions and its details remain largely unknown. In particular, the duration of chronological overlap between the two groups is much debated, as are the implications of this overlap for the nature of the biological and cultural interactions between Neanderthals and H. sapiens. Here we report the discovery and direct dating of human remains found in association with Initial Upper Palaeolithic artefacts[2], from excavations at Bacho Kiro Cave (Bulgaria). Morphological analysis of a tooth and mitochondrial DNA from several hominin bone fragments, identified through proteomic screening, assign these finds to H. sapiens and link the expansion of Initial Upper Palaeolithic technologies with the spread of H. sapiens into the mid-latitudes of Eurasia before 45 thousand years ago[3]. The excavations yielded a wealth of bone artefacts, including pendants manufactured from cave bear teeth that are reminiscent of those later produced by the last Neanderthals of western Europe[4-6]. These finds are consistent with models based on the arrival of multiple waves of H. sapiens into Europe coming into contact with declining Neanderthal populations[7,8].}, }
@article {pmid32409455, year = {2020}, author = {Gibbons, A}, title = {Oldest Homo sapiens bones found in Europe.}, journal = {Science (New York, N.Y.)}, volume = {368}, number = {6492}, pages = {697}, doi = {10.1126/science.368.6492.697}, pmid = {32409455}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Bone and Bones ; Bulgaria ; Humans ; Molar/anatomy &amp; histology ; *Neanderthals ; }, }
@article {pmid32398823, year = {2020}, author = {Hardy, BL and Moncel, MH and Kerfant, C and Lebon, M and Bellot-Gurlet, L and Mélard, N}, title = {Author Correction: Direct evidence of Neanderthal fibre technology and its cognitive and behavioral implications.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8167}, doi = {10.1038/s41598-020-65143-5}, pmid = {32398823}, issn = {2045-2322}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32385291, year = {2020}, author = {Martisius, NL and Welker, F and Dogandžić, T and Grote, MN and Rendu, W and Sinet-Mathiot, V and Wilcke, A and McPherron, SJP and Soressi, M and Steele, TE}, title = {Non-destructive ZooMS identification reveals strategic bone tool raw material selection by Neandertals.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {7746}, pmid = {32385291}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; *Bone and Bones ; *Neanderthals ; *Tool Use Behavior ; }, abstract = {Five nearly identical fragments of specialized bone tools, interpreted as lissoirs (French for "smoothers"), have been found at two Middle Paleolithic sites in southwest France. The finds span three separate archaeological deposits, suggesting continuity in the behavior of late Neandertals. Using standard morphological assessments, we determined that the lissoirs were produced on ribs of medium-sized ungulates. However, since these bones are highly fragmented and anthropogenically modified, species determinations were challenging. Also, conservative curation policy recommends minimizing destructive sampling of rare, fragile, or small artifacts for molecular identification methods. To better understand raw material selection for these five lissoirs, we reassess their taxonomy using a non-destructive ZooMS methodology based on triboelectric capture of collagen. We sampled four storage containers and obtained identifiable MALDI-TOF MS collagen fingerprints, all indicative of the same taxonomic clade, which includes aurochs and bison (Bos sp. and Bison sp.). The fifth specimen, which was stored in a plastic bag, provided no useful MALDI-TOF MS spectra. We show that the choice of large bovid ribs in an archaeological layer dominated by reindeer (Rangifer tarandus) demonstrates strategic selection by these Neandertals. Furthermore, our results highlight the value of a promising technique for the non-destructive analysis of bone artifacts.}, }
@article {pmid32380300, year = {2020}, author = {Verna, C and Détroit, F and Kupczik, K and Arnaud, J and Balzeau, A and Grimaud-Hervé, D and Bertrand, S and Riou, B and Moncel, MH}, title = {The Middle Pleistocene hominin mandible from Payre (Ardèche, France).}, journal = {Journal of human evolution}, volume = {144}, number = {}, pages = {102775}, doi = {10.1016/j.jhevol.2020.102775}, pmid = {32380300}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Fossils ; France ; Hominidae/*anatomy &amp; histology ; Mandible/*anatomy &amp; histology ; Neanderthals/anatomy &amp; histology ; }, abstract = {Although Neandertals are the best-known fossil hominins, the tempo and evolutionary processes in their lineage are strongly debated. This is in part due to the scarcity of the fossil record, in particular before the marine isotopic stage (MIS) 5. In 2010, a partial hominin mandible was discovered at the Middle Paleolithic site of Payre (France) in a layer that is dated to the end of MIS 8/beginning of MIS 7, a time period for which very few fossils are known in Europe. The Payre 15 mandible retains the complete symphyseal region and right lateral corpus with heavily worn P4, M1, and M2 in situ. Taphonomic modifications in the form of three notches suggest that this individual was chewed by a carnivore. We provide here the first detailed description of this specimen and a comparative analysis that includes morphological features, linear mandibular dimensions, an elliptic Fourier analysis of the symphysis, and a morphometric analysis of the M1 roots (based on segmented CT scan data). Our comparative sample encompasses European Middle and Upper Pleistocene specimens attributed to Homo heidelbergensis and Homo neanderthalensis, Upper Pleistocene Homo sapiens, and Holocene Homo sapiens. The Payre 15 mandible shows a combination of primitive and Neandertal-like features, with a receding symphyseal profile without any element of the mentum osseum, a posterior location of the mental foramen and lateral prominence. Its mandibular body is tall and thick anteriorly. Payre 15 has mesotaurodont M1 roots and a three-rooted M2. By its dimensions and combination of features, Payre 15 aligns better with Middle Pleistocene European hominins than with MIS 6-3 Neandertals. Noteworthy, it falls well within the range of variation of the Sima de los Huesos sample. Our results underscore that the total pattern of Neandertal-derived morphology was not achieved at the beginning of the MIS 7 and suggest a low level of mandibular diachronic changes for the period MIS 11-7.}, }
@article {pmid32371290, year = {2020}, author = {Yeshurun, R and Malkinson, D and Crater Gershtein, KM and Zaidner, Y and Weinstein-Evron, M}, title = {Site occupation dynamics of early modern humans at Misliya Cave (Mount Carmel, Israel): Evidence from the spatial taphonomy of faunal remains.}, journal = {Journal of human evolution}, volume = {143}, number = {}, pages = {102797}, doi = {10.1016/j.jhevol.2020.102797}, pmid = {32371290}, issn = {1095-8606}, mesh = {*Archaeology ; Caves ; *Feeding Behavior ; *Food Handling ; Fossils ; Humans ; Israel ; }, abstract = {Space use in Middle Paleolithic (MP) camps has been suggested as a source of information on the intensity and repetition of occupations and, by extension, of demographics. In the Levant, clear evidence for differential intrasite use and maintenance was important in viewing the late MP Neanderthal sites as base camps inhabited for a significant duration, relative to the Early MP (EMP). We test this model with the rich faunal assemblage from the EMP (>140 ka) site of Misliya Cave, Mount Carmel, Israel. Excavations in Misliya yielded a large and diverse lithic assemblage, combustion features, and a modern human maxilla, together with a large archaeofaunal assemblage that we use as a spatial marker. We analyzed the distribution of bone items with variable taphonomic properties (anthropogenic, biogenic, and abiotic bone-surface modifications) in a hearth-related context, both by comparing grid squares and point patterns. Both analyses are largely congruent. They indicate repeated and consistent use of the site's space that includes hearth-related consumption activities and peripheral activities further away, albeit with little evidence for site maintenance. Thus, the Misliya results display a mixed signal of clear around-the-fire pattern and differential space use in the EMP that is reminiscent of the much later MP sites in the Levant, but without the more elaborate camp maintenance. More case studies and detailed proxies are needed before we can fine-tune our understanding of camp structure in the Levantine MP and its bearing to site occupation dynamics.}, }
@article {pmid32356723, year = {2020}, author = {Jordan, B}, title = {[Neandertal DNA in Africans].}, journal = {Medecine sciences : M/S}, volume = {36}, number = {4}, pages = {421-423}, doi = {10.1051/medsci/2020055}, pmid = {32356723}, issn = {1958-5381}, mesh = {Africa ; Animals ; DNA/analysis/*genetics ; Evolution, Molecular ; Genetics, Population ; Genome ; History, 21st Century ; History, Ancient ; Hominidae/classification/*genetics ; Humans ; Hybridization, Genetic ; Neanderthals/classification/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {Sophisticated analyses of current human populations compared to a high-coverage Neandertal genome sequence indicate that, contrary to the previous consensus, African genomes carry a small but significant amount of Neandertal-specific DNA. This indicates back-migration into Africa of modern humans (carrying some Neandertal sequences) and underlines the complexity of ancient human migrations.}, }
@article {pmid32344263, year = {2020}, author = {Shimelmitz, R and Kuhn, SL and Weinstein-Evron, M}, title = {The evolution of raw material procurement strategies: A view from the deep sequence of Tabun Cave, Israel.}, journal = {Journal of human evolution}, volume = {143}, number = {}, pages = {102787}, doi = {10.1016/j.jhevol.2020.102787}, pmid = {32344263}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; Caves ; *Cultural Evolution ; Humans ; Israel ; Neanderthals/*psychology ; *Technology ; *Tool Use Behavior ; }, abstract = {Changes in the ways Paleolithic foragers exploited raw material sources are linked to mobility, the demands of production, and investment in quarrying. Here, we analyze the use of raw materials in a long series of superimposed layers from Tabun Cave dating to the Middle Pleistocene, attributed to the Lower and Middle Paleolithic periods. Using the cortex preserved on the surfaces of artifacts, including blanks, tools and cores, we distinguished between flints obtained from primary and secondary geological contexts. The results from Tabun Cave indicate that the exploitation of secondary sources was fairly common during the earlier part of the Lower Paleolithic sequence. It decreased during the later part of the Acheulo-Yabrudian complex of the Lower Paleolithic, coinciding with growing use of predetermined technological strategies, which demand high-quality raw materials. By the Middle Paleolithic, primary and secondary raw materials are generally designated for different reduction trajectories, suggesting a growing distinction and formalization of technological strategies. The need for the 'best' stone for Middle Paleolithic laminar and Levallois production may have necessitated increased investment in raw material procurement. During most of the Lower Paleolithic, raw material needs could have been met easily through a purely embedded strategy, in which raw material was collected while focusing on other activities. Starting in the late Acheulo-Yabrudian and especially during the Middle Paleolithic, the focus on primary geological contexts may have demanded greater planning of visits to raw material outcrops. In other words, in the Middle Paleolithic and possibly already during the very end of the Lower Paleolithic, raw material procurement had greater influence on patterns of movement through the landscape.}, }
@article {pmid32330268, year = {2020}, author = {Lodewijk, GA and Fernandes, DP and Vretzakis, I and Savage, JE and Jacobs, FMJ}, title = {Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels.}, journal = {Molecular biology and evolution}, volume = {37}, number = {9}, pages = {2531-2548}, pmid = {32330268}, issn = {1537-1719}, mesh = {Animals ; *Biological Evolution ; Genome, Human ; Genomic Structural Variation ; Humans ; Multigene Family ; Neanderthals/*genetics ; Receptor, Notch2/*genetics/metabolism ; }, abstract = {Ever since the availability of genomes from Neanderthals, Denisovans, and ancient humans, the field of evolutionary genomics has been searching for protein-coding variants that may hold clues to how our species evolved over the last ∼600,000 years. In this study, we identify such variants in the human-specific NOTCH2NL gene family, which were recently identified as possible contributors to the evolutionary expansion of the human brain. We find evidence for the existence of unique protein-coding NOTCH2NL variants in Neanderthals and Denisovans which could affect their ability to activate Notch signaling. Furthermore, in the Neanderthal and Denisovan genomes, we find unusual NOTCH2NL configurations, not found in any of the modern human genomes analyzed. Finally, genetic analysis of archaic and modern humans reveals ongoing adaptive evolution of modern human NOTCH2NL genes, identifying three structural variants acting complementary to drive our genome to produce a lower dosage of NOTCH2NL protein. Because copy-number variations of the 1q21.1 locus, encompassing NOTCH2NL genes, are associated with severe neurological disorders, this seemingly contradicting drive toward low levels of NOTCH2NL protein indicates that the optimal dosage of NOTCH2NL may have not yet been settled in the human population.}, }
@article {pmid32318238, year = {2020}, author = {Zeng, Y and Pu, X and Du, J and Yang, X and Li, X and Mandal, MSN and Yang, T and Yang, J}, title = {Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases.}, journal = {Oxidative medicine and cellular longevity}, volume = {2020}, number = {}, pages = {3836172}, pmid = {32318238}, issn = {1942-0994}, mesh = {Antioxidants/*chemistry ; Chronic Disease/*therapy ; Hordeum/*chemistry ; Humans ; }, abstract = {Barley plays an important role in health and civilization of human migration from Africa to Asia, later to Eurasia. We demonstrated the systematic mechanism of functional ingredients in barley to combat chronic diseases, based on PubMed, CNKI, and ISI Web of Science databases from 2004 to 2020. Barley and its extracts are rich in 30 ingredients to combat more than 20 chronic diseases, which include the 14 similar and 9 different chronic diseases between grains and grass, due to the major molecular mechanism of six functional ingredients of barley grass (GABA, flavonoids, SOD, K-Ca, vitamins, and tryptophan) and grains (β-glucans, polyphenols, arabinoxylan, phytosterols, tocols, and resistant starch). The antioxidant activity of barley grass and grain has the same and different functional components. These results support findings that barley grain and its grass are the best functional food, promoting ancient Babylonian and Egyptian civilizations, and further show the depending functional ingredients for diet from Pliocene hominids in Africa and Neanderthals in Europe to modern humans in the world. This review paper not only reveals the formation and action mechanism of barley diet overcoming human chronic diseases, but also provides scientific basis for the development of health products and drugs for the prevention and treatment of human chronic diseases.}, }
@article {pmid32299352, year = {2020}, author = {Moriano, J and Boeckx, C}, title = {Modern human changes in regulatory regions implicated in cortical development.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {304}, pmid = {32299352}, issn = {1471-2164}, mesh = {Animals ; Cerebral Cortex/*growth &amp; development ; Chromatin/genetics/metabolism ; *Enhancer Elements, Genetic ; Gene Expression Regulation, Developmental ; Histone-Lysine N-Methyltransferase/genetics/metabolism ; Hominidae/*genetics ; Humans ; Neanderthals/*genetics ; Neurogenesis/*genetics ; Polymorphism, Single Nucleotide ; *Promoter Regions, Genetic ; Species Specificity ; Wnt Signaling Pathway/genetics ; }, abstract = {BACKGROUND: Recent paleogenomic studies have highlighted a very small set of proteins carrying modern human-specific missense changes in comparison to our closest extinct relatives. Despite being frequently alluded to as highly relevant, species-specific differences in regulatory regions remain understudied. Here, we integrate data from paleogenomics, chromatin modification and physical interaction, and single-cell gene expression of neural progenitor cells to identify derived regulatory changes in the modern human lineage in comparison to Neanderthals/Denisovans. We report a set of genes whose enhancers and/or promoters harbor modern human single nucleotide changes and are active at early stages of cortical development.<br><br>RESULTS: We identified 212 genes controlled by regulatory regions harboring modern human changes where Neanderthals/Denisovans carry the ancestral allele. These regulatory regions significantly overlap with putative modern human positively-selected regions and schizophrenia-related genetic loci. Among the 212 genes, we identified a substantial proportion of genes related to transcriptional regulation and, specifically, an enrichment for the SETD1A histone methyltransferase complex, known to regulate WNT signaling for the generation and proliferation of intermediate progenitor cells.<br><br>CONCLUSIONS: This study complements previous research focused on protein-coding changes distinguishing our species from Neanderthals/Denisovans and highlights chromatin regulation as a functional category so far overlooked in modern human evolution studies. We present a set of candidates that will help to illuminate the investigation of modern human-specific ontogenetic trajectories.}, }
@article {pmid32286344, year = {2020}, author = {Radovčić, D and Birarda, G and Sršen, AO and Vaccari, L and Radovčić, J and Frayer, DW}, title = {Surface analysis of an eagle talon from Krapina.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {6329}, pmid = {32286344}, issn = {2045-2322}, abstract = {The Krapina white-tailed eagle talons represent a kind of jewelry worn by Krapina Neandertals some 130,000 years ago. New inspection of one Krapina talon (386.1) revealed a fiber, sealed by a thin silicate coating, adhering to the surface within a wide cut mark, as well as concentrated traces of occasional spots of red and yellow pigment and some black stains. We analyzed the fiber and small portions of pigmented areas by non-invasive, infrared synchrotron beam. Different areas were targeted, revealing the protein nature of the fiber, identified as of animal origin. Targeted areas revealed intra- and inter-strand aggregation indicating the fiber to be collagen losing its original triple α-helix conformation, further confirming the diagenetic decay of the original collagen structure and the antiquity of the fiber. It is possible that the fiber is a remnant of the leather or sinew string binding the talons together. Spectroscopic analysis of the pigments in two isolated areas confirmed two types of ochre and that the dark spots are charcoal remnants. Applying novel non-invasive technologies provides new possibilities to further test the hypothesis of using prehistoric objects for symbolic purposes.}, }
@article {pmid32285198, year = {2020}, author = {Barreiro, LB and Quintana-Murci, L}, title = {Evolutionary and population (epi)genetics of immunity to infection.}, journal = {Human genetics}, volume = {139}, number = {6-7}, pages = {723-732}, pmid = {32285198}, issn = {1432-1203}, support = {R01 GM115656/GM/NIGMS NIH HHS/United States ; R01-GM115656/GM/NIGMS NIH HHS/United States ; R01-GM134376/GM/NIGMS NIH HHS/United States ; R01 GM134376/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; *Epigenesis, Genetic ; *Genetic Variation ; *Genetics, Population ; *Genome, Human ; Humans ; Infections/epidemiology/genetics/*immunology ; Selection, Genetic ; }, abstract = {Immune response is one of the functions that have been more strongly targeted by natural selection during human evolution. The evolutionary genetic dissection of the immune system has greatly helped to distinguish genes and functions that are essential, redundant or advantageous for human survival. It is also becoming increasingly clear that admixture between early Eurasians with now-extinct hominins such as Neanderthals or Denisovans, or admixture between modern human populations, can be beneficial for human adaptation to pathogen pressures. In this review, we discuss how the integration of population genetics with functional genomics in diverse human populations can inform about the changes in immune functions related to major lifestyle transitions (e.g., from hunting and gathering to farming), the action of natural selection to the evolution of the immune system, and the history of past epidemics. We also highlight the need of expanding the characterization of the immune system to a larger array of human populations-particularly neglected human groups historically exposed to different pathogen pressures-to fully capture the relative contribution of genetic, epigenetic, and environmental factors to immune response variation in humans.}, }
@article {pmid32273518, year = {2020}, author = {Hardy, BL and Moncel, MH and Kerfant, C and Lebon, M and Bellot-Gurlet, L and Mélard, N}, title = {Direct evidence of Neanderthal fibre technology and its cognitive and behavioral implications.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4889}, pmid = {32273518}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Cellulose/analysis ; *Cognition ; *Fossils ; France ; History, Ancient ; Lignin/analysis ; Microscopy, Electron, Scanning ; Neanderthals/*psychology ; Soil/chemistry ; Spectroscopy, Fourier Transform Infrared ; Spectrum Analysis, Raman ; Technology/*history ; Textiles/analysis/*history ; }, abstract = {Neanderthals are often considered as less technologically advanced than modern humans. However, we typically only find faunal remains or stone tools at Paleolithic sites. Perishable materials, comprising the vast majority of material culture items, are typically missing. Individual twisted fibres on stone tools from the Abri du Maras led to the hypothesis of Neanderthal string production in the past, but conclusive evidence was lacking. Here we show direct evidence of fibre technology in the form of a 3-ply cord fragment made from inner bark fibres on a stone tool recovered in situ from the same site. Twisted fibres provide the basis for clothing, rope, bags, nets, mats, boats, etc. which, once discovered, would have become an indispensable part of daily life. Understanding and use of twisted fibres implies the use of complex multi-component technology as well as a mathematical understanding of pairs, sets, and numbers. Added to recent evidence of birch bark tar, art, and shell beads, the idea that Neanderthals were cognitively inferior to modern humans is becoming increasingly untenable.}, }
@article {pmid32269345, year = {2020}, author = {Welker, F and Ramos-Madrigal, J and Gutenbrunner, P and Mackie, M and Tiwary, S and Rakownikow Jersie-Christensen, R and Chiva, C and Dickinson, MR and Kuhlwilm, M and de Manuel, M and Gelabert, P and Martinón-Torres, M and Margvelashvili, A and Arsuaga, JL and Carbonell, E and Marques-Bonet, T and Penkman, K and Sabidó, E and Cox, J and Olsen, JV and Lordkipanidze, D and Racimo, F and Lalueza-Fox, C and Bermúdez de Castro, JM and Willerslev, E and Cappellini, E}, title = {The dental proteome of Homo antecessor.}, journal = {Nature}, volume = {580}, number = {7802}, pages = {235-238}, pmid = {32269345}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Dental Enamel/*chemistry/*metabolism ; *Fossils ; Georgia (Republic) ; *Hominidae ; Humans ; Male ; Molar/chemistry/metabolism ; Neanderthals ; Phosphoproteins/analysis/chemistry/metabolism ; Phosphorylation ; Phylogeny ; Proteome/*analysis/chemistry/*metabolism ; Spain ; }, abstract = {The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated[1-5]. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge[6-8]. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)[9,10] and Homo erectus from Dmanisi (Georgia)[1], two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor-that is, similar to that of modern humans-may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.}, }
@article {pmid32268436, year = {2020}, author = {Merseburger, AS and Rüssel, C and Belz, H and Spiegelhalder, P and Feyerabend, S and Tran, N and Kruetzfeldt, K and Baurecht, W and Bögemann, M}, title = {[Early- vs. late-onset treatment using abiraterone acetate plus prednisone in chemo-naïve, asymptomatic or mildly symptomatic patients with metastatic CRPC after androgen deprivation therapy].}, journal = {Aktuelle Urologie}, volume = {51}, number = {6}, pages = {562-571}, doi = {10.1055/a-1121-7593}, pmid = {32268436}, issn = {1438-8820}, mesh = {*Abiraterone Acetate/therapeutic use ; Androgen Antagonists/adverse effects ; Androgens/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Cohort Studies ; Humans ; Male ; Prednisone/adverse effects ; Prospective Studies ; *Prostatic Neoplasms, Castration-Resistant/drug therapy ; Retrospective Studies ; Treatment Outcome ; }, abstract = {BACKGROUND: Abiraterone acetate (AA) is a prodrug of abiraterone, which is an irreversible inhibitor of 17α-hydroxylase/C17, 20-lyase. Since 2011, abiraterone acetate has been available in combination with prednisone/prednisolone (AA + P) for the treatment of metastatic castration-resistant prostate cancer (mCRPC) after pre-treatment with docetaxel, and since 2012 for the treatment of chemotherapy-naïve asymptomatic or mildly symptomatic mCRPC patients. A revision of the guidelines of the European Association of Urology in 2014 redefining castration resistance gave rise to the question of when the treatment of mCRPC with abiraterone acetate plus prednisone should be initiated after prior hormone treatment and how successful it would be. This led us to observe an early-onset AA + P therapy cohort (EC) and a late-onset therapy cohort (LC) of patients.<br><br>PATIENTS AND METHODS: &#x2002;We designed a combined retrospective and prospective, multicentre, non-interventional two-cohort study to obtain data on the effectiveness and safety of an early-onset AA&#x200a;+&#x200a;P therapy in mCRPC patients in the clinical routine compared to a late therapy onset. The EC comprised patients who received AA&#x200a;+&#x200a;P immediately after castration resistance without a prior first-generation antiandrogen such as bicalutamide or flutamide. The LC included patients who, after castration resistance had occurred, started treatment with AA&#x200a;+&#x200a;P only after unsuccessful treatment with a first-generation antiandrogen. Patients with mCRPC who received AA&#x200a;+&#x200a;P therapy according to the physician's routine clinical practice decision were considered. The patients were consecutively included in the study on the basis of their medical records, with the treatment decision having been made independently of and before patient enrolment. Patients were documented or followed from the beginning of AA&#x200a;+&#x200a;P therapy until the start of a carcinoma-specific systemic follow-up therapy (retrospectively if before and prospectively if after start of data collection). Effectiveness analyses were done for all patients with at least two AA&#x200a;+&#x200a;P administrations and safety analyses for all treated patients.<br><br>RESULTS: &#x2002;Of the 159 patients included, 44 received early therapy and 105 received later therapy with AA&#x200a;+&#x200a;P. 10 patients could not be clearly assigned and were summarised in a third cohort (missed early-onset therapy assignment; MEC). 56/159 patients (35.2&#x200a;%) were still alive at study start and 103/159 patients (64.8&#x200a;%) had already deceased (31/44 [70.5&#x200a;%] in EC, 64/105 [61.0&#x200a;%] in LC, and 8/10 [80.0&#x200a;%] in MEC). 24/159 patients (15.1&#x200a;%) were documented both retrospectively and prospectively. The median duration of AA&#x200a;+&#x200a;P treatment was 11.3 months for EC, 12.0 months for LC, and 8.3 months for MEC patients. The median time to next systemic cancer therapy or death was 12.3 months for EC and 12.8 months for LC patients (p&#x200a;=&#x200a;0.2820). The median time to the next systemic cancer therapy alone (i.&#x200a;e. without the event 'death') was 22.7 months for EC and 23.3 months for LC patients (p&#x200a;=&#x200a;0.5995). Median overall survival (OS) was 22.3 months for EC and 39.2 months for LC patients (p&#x200a;=&#x200a;0.0232). The incidence of serious adverse events (SAEs) was low. SAEs occurred in 3/44 EC (6.8&#x200a;%), 4/105 LC (3.8&#x200a;%), and 1/10 MEC patients (10.0&#x200a;%). One SAE in EC and one in LC resulted in death.<br><br>CONCLUSIONS: &#x2002;In contrast to the new definition of castration resistance, AA&#x200a;+&#x200a;P was still more frequently used in daily clinical practice during the study observation period in patients treated with antiandrogens of the first generation after occurrence of castration resistance. Nevertheless, AA&#x200a;+&#x200a;P therapy appears to be effective and well tolerated during clinical routine in mCRPC patients. A comparison of the study results with earlier 'real-world' studies, however, has to take limiting factors into account. The observed difference in median overall survival might be explained by the imbalance of baseline characteristics between both cohorts with regard to number of patients, patients already deceased at start of documentation, patients with visceral metastases and patients with opioids at start of AA&#x200a;+&#x200a;P. For these reasons, patients in the EC initially might have had a poorer prognosis. A prospective randomised and controlled clinical trial would therefore be necessary to assess a possible difference in overall survival and response of the AA&#x200a;+&#x200a;P treatment with respect to therapy onset.}, }
@article {pmid32247528, year = {2021}, author = {Grimaud-Hervé, D and Albessard-Ball, L and Pokhojaev, A and Balzeau, A and Sarig, R and Latimer, B and McDermott, Y and May, H and Hershkovitz, I}, title = {The endocast of the late Middle Paleolithic Manot 1 specimen, Western Galilee, Israel.}, journal = {Journal of human evolution}, volume = {160}, number = {}, pages = {102734}, doi = {10.1016/j.jhevol.2019.102734}, pmid = {32247528}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Fossils ; *Hominidae ; Humans ; Israel ; *Neanderthals ; Skull/anatomy &amp; histology ; }, abstract = {Studying endocasts has long allowed anthropologists to examine changes in the external topography and the overall size of the brain throughout the evolutionary history of hominins. The nearly complete calvaria of Manot 1 presents an opportunity to gain insights into the external brain morphology, vascular system, and dimensions of the brain of this late Middle Paleolithic hominin. Detailed size and shape analyses of the Manot 1 endocast indicate a modern Homo sapiens anatomy, despite the presence of some primitive features of the calvaria. Traits considered to be derived endocranial features for H. sapiens are present in Manot 1, including an elongated parietal sagittal chord with an elevated superior part of the hemisphere, a widened posterior part of the frontal lobes, a considerable development of the parietal reliefs such as the supramarginal lobules, and a slight posterior projection of the occipital lobes. These findings, together with data presented in previous studies, rule out the possibility of a direct Neanderthal ancestry for the Manot 1 hominin and instead confirm its affiliation with H. sapiens. The Manot 1 calvaria is more similar to that of later Upper Paleolithic H. sapiens than it is to the earlier Levantine populations of Skhul and Qafzeh. The late Middle Paleolithic date of Manot 1 provides an opportunity to analyze the recent developments in human cerebral morphology and organization.}, }
@article {pmid32247107, year = {2020}, author = {Pereira-Pedro, AS and Bruner, E and Gunz, P and Neubauer, S}, title = {A morphometric comparison of the parietal lobe in modern humans and Neanderthals.}, journal = {Journal of human evolution}, volume = {142}, number = {}, pages = {102770}, doi = {10.1016/j.jhevol.2020.102770}, pmid = {32247107}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Humans ; Neanderthals/*anatomy &amp; histology ; Parietal Lobe/*anatomy &amp; histology ; }, abstract = {The modern human brain and braincase have a characteristic globular shape including parietal and cerebellar bulging. In contrast, Neanderthals, although having similar endocranial volume, displayed more elongated endocrania with flatter parietal and cerebellar regions. Based on endocranial imprints, we compare the parietal lobe morphology of modern humans and Neanderthals, as this brain region is central to several cognitive functions including tool use and visual imaging. In paleoneurology, shape analyses of endocasts are based either on anatomical landmarks that represent endocranial surface features homologous to cortical convolutions (impressions of brain gyri and sulci) or on dense meshes of semilandmarks that capture overall endocranial shape. Previous analyses using the former suggested that modern humans have relatively longer and taller parietal lobes than extinct human species, while the latter emphasized parietal bulging without a significant size difference of parietal regions. In the present study, we combine both anatomical landmarks and surface semilandmarks to investigate the morphological differences of the parietal lobes between modern humans and Neanderthals. Despite limitations by landmark uncertainty, our analyses were able to detect and confirm average different parietal shapes, with modern humans displaying taller and anteroposteriorly extended parietal lobes. We also show mean size differences, with modern humans displaying slightly larger surface areas on the dorsal posterior parietal region, and on a lateral region comprising the supramarginal gyrus, angular gyrus, and intraparietal sulcus. While we observed average differences in the parietal form between the two species, their ranges of distribution overlap, indicating the differences could be a matter of degree. Thus, further analyses on intraspecific variation in parietal lobe morphology within modern human brains should help understand the differences between globular and elongated endocrania. This is crucial because changes to the parietal cortex might affect associative and integrative functions between somatic and visual primary inputs.}, }
@article {pmid32240884, year = {2020}, author = {Sorrentino, R and Carlson, KJ and Bortolini, E and Minghetti, C and Feletti, F and Fiorenza, L and Frost, S and Jashashvili, T and Parr, W and Shaw, C and Su, A and Turley, K and Wroe, S and Ryan, TM and Belcastro, MG and Benazzi, S}, title = {Morphometric analysis of the hominin talus: Evolutionary and functional implications.}, journal = {Journal of human evolution}, volume = {142}, number = {}, pages = {102747}, doi = {10.1016/j.jhevol.2020.102747}, pmid = {32240884}, issn = {1095-8606}, support = {724046/ERC_/European Research Council/International ; }, mesh = {Animals ; *Biological Evolution ; Female ; Fossils/anatomy &amp; histology ; Gorilla gorilla/anatomy &amp; histology/physiology ; Hominidae/*anatomy &amp; histology/*physiology ; Humans ; *Locomotion ; Male ; Neanderthals/anatomy &amp; histology/physiology ; Pan troglodytes/anatomy &amp; histology/physiology ; Talus/*anatomy &amp; histology ; }, abstract = {The adoption of bipedalism is a key benchmark in human evolution that has impacted talar morphology. Here, we investigate talar morphological variability in extinct and extant hominins using a 3D geometric morphometric approach. The evolutionary timing and appearance of modern human-like features and their contributions to bipedal locomotion were evaluated on the talus as a whole, each articular facet separately, and multiple combinations of facets. Distinctive suites of features are consistently present in all fossil hominins, despite the presence of substantial interspecific variation, suggesting a potential connection of these suites to bipedal gait. A modern human-like condition evolved in navicular and lateral malleolar facets early in the hominin lineage compared with other facets, which demonstrate more complex morphological variation within Homininae. Interestingly, navicular facet morphology of Australopithecus afarensis is derived in the direction of Homo, whereas more recent hominin species such as Australopithecus africanus and Australopithecus sediba retain more primitive states in this facet. Combining the navicular facet with the trochlea and the posterior calcaneal facet as a functional suite, however, distinguishes Australopithecus from Homo in that the medial longitudinal arch had not fully developed in the former. Our results suggest that a more everted foot and stiffer medial midtarsal region are adaptations that coincide with the emergence of bipedalism, whereas a high medial longitudinal arch emerges later in time, within Homo. This study provides novel insights into the emergence of talar morphological traits linked to bipedalism and its transition from a facultative to an obligate condition.}, }
@article {pmid32234956, year = {2020}, author = {Taskent, O and Lin, YL and Patramanis, I and Pavlidis, P and Gokcumen, O}, title = {Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage.}, journal = {Genetics}, volume = {215}, number = {2}, pages = {497-509}, pmid = {32234956}, issn = {1943-2631}, mesh = {Animals ; *Genetics, Population ; Genome, Human ; *Haplotypes ; Hominidae ; Humans ; Neanderthals/*genetics ; *Phenotype ; *Polymorphism, Genetic ; Russia ; *Selection, Genetic ; }, abstract = {The time, extent, and genomic effect of the introgressions from archaic humans into ancestors of extant human populations remain some of the most exciting venues of population genetics research in the past decade. Several studies have shown population-specific signatures of introgression events from Neanderthals, Denisovans, and potentially other unknown hominin populations in different human groups. Moreover, it was shown that these introgression events may have contributed to phenotypic variation in extant humans, with biomedical and evolutionary consequences. In this study, we present a comprehensive analysis of the unusually divergent haplotypes in the Eurasian genomes and show that they can be traced back to multiple introgression events. In parallel, we document hundreds of deletion polymorphisms shared with Neanderthals. A locus-specific analysis of one such shared deletion suggests the existence of a direct introgression event from the Altai Neanderthal lineage into the ancestors of extant East Asian populations. Overall, our study is in agreement with the emergent notion that various Neanderthal populations contributed to extant human genetic variation in a population-specific manner.}, }
@article {pmid32217711, year = {2020}, author = {Will, M}, title = {Neanderthal surf and turf.}, journal = {Science (New York, N.Y.)}, volume = {367}, number = {6485}, pages = {1422-1423}, doi = {10.1126/science.abb3568}, pmid = {32217711}, issn = {1095-9203}, mesh = {Animals ; Fossils ; *Hominidae ; *Neanderthals ; }, }
@article {pmid32217702, year = {2020}, author = {Zilhão, J and Angelucci, DE and Igreja, MA and Arnold, LJ and Badal, E and Callapez, P and Cardoso, JL and d'Errico, F and Daura, J and Demuro, M and Deschamps, M and Dupont, C and Gabriel, S and Hoffmann, DL and Legoinha, P and Matias, H and Monge Soares, AM and Nabais, M and Portela, P and Queffelec, A and Rodrigues, F and Souto, P}, title = {Last Interglacial Iberian Neandertals as fisher-hunter-gatherers.}, journal = {Science (New York, N.Y.)}, volume = {367}, number = {6485}, pages = {}, doi = {10.1126/science.aaz7943}, pmid = {32217702}, issn = {1095-9203}, mesh = {Animal Shells ; Animals ; Archaeology ; Atlantic Ocean ; Birds ; Caves ; *Diet ; Fishes ; Mammals ; *Neanderthals ; Nuts ; Pinus ; Portugal ; Seafood ; Turtles ; }, abstract = {Marine food-reliant subsistence systems such as those in the African Middle Stone Age (MSA) were not thought to exist in Europe until the much later Mesolithic. Whether this apparent lag reflects taphonomic biases or behavioral distinctions between archaic and modern humans remains much debated. Figueira Brava cave, in the Arrábida range (Portugal), provides an exceptionally well preserved record of Neandertal coastal resource exploitation on a comparable scale to the MSA and dated to ~86 to 106 thousand years ago. The breadth of the subsistence base-pine nuts, marine invertebrates, fish, marine birds and mammals, tortoises, waterfowl, and hoofed game-exceeds that of regional early Holocene sites. Fisher-hunter-gatherer economies are not the preserve of anatomically modern people; by the Last Interglacial, they were in place across the Old World in the appropriate settings.}, }
@article {pmid32193295, year = {2020}, author = {Bergström, A and McCarthy, SA and Hui, R and Almarri, MA and Ayub, Q and Danecek, P and Chen, Y and Felkel, S and Hallast, P and Kamm, J and Blanché, H and Deleuze, JF and Cann, H and Mallick, S and Reich, D and Sandhu, MS and Skoglund, P and Scally, A and Xue, Y and Durbin, R and Tyler-Smith, C}, title = {Insights into human genetic variation and population history from 929 diverse genomes.}, journal = {Science (New York, N.Y.)}, volume = {367}, number = {6484}, pages = {}, pmid = {32193295}, issn = {1095-9203}, support = {/ERC_/European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; 206194/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; //Medical Research Council,/International ; FC001595/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; FC001595/MRC_/Medical Research Council/United Kingdom ; 207492/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa ; Americas ; Animals ; Asia ; DNA Copy Number Variations ; *Genetic Variation ; *Genetics, Population ; *Genome, Human ; Haplotypes ; Hominidae/genetics ; Humans ; INDEL Mutation ; Neanderthals/genetics ; Oceania ; Phylogeny ; Polymorphism, Single Nucleotide ; Population Density ; Racial Groups/genetics ; *Whole Genome Sequencing ; }, abstract = {Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.}, }
@article {pmid32170098, year = {2020}, author = {Modesto-Mata, M and Dean, MC and Lacruz, RS and Bromage, TG and García-Campos, C and Martínez de Pinillos, M and Martín-Francés, L and Martinón-Torres, M and Carbonell, E and Arsuaga, JL and Bermúdez de Castro, JM}, title = {Short and long period growth markers of enamel formation distinguish European Pleistocene hominins.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4665}, pmid = {32170098}, issn = {2045-2322}, mesh = {Animals ; Biological Evolution ; *Biomarkers ; Dental Enamel/*anatomy &amp; histology/growth &amp; development/metabolism ; *Fossils ; *Hominidae ; Humans ; Microscopy, Confocal ; *Osteogenesis ; Tooth/anatomy &amp; histology/growth &amp; development/metabolism ; }, abstract = {Characterizing dental development in fossil hominins is important for distinguishing between them and for establishing where and when the slow overall growth and development of modern humans appeared. Dental development of australopiths and early Homo was faster than modern humans. The Atapuerca fossils (Spain) fill a barely known gap in human evolution, spanning ~1.2 to ~0.4 million years (Ma), during which H. sapiens and Neandertal dental growth characteristics may have developed. We report here perikymata counts, perikymata distributions and periodicities of all teeth belonging to the TE9 level of Sima del Elefante, level TD6.2 of Gran Dolina (H. antecessor) and Sima de los Huesos. We found some components of dental growth in the Atapuerca fossils resembled more recent H. sapiens. Mosaic evolution of perikymata counts and distribution generate three distinct clusters: H. antecessor, Sima de los Huesos and H. sapiens.}, }
@article {pmid32163763, year = {2020}, author = {Belcastro, MG and Mariotti, V and Pietrobelli, A and Sorrentino, R and García-Tabernero, A and Estalrrich, A and Rosas, A}, title = {The study of the lower limb entheses in the Neanderthal sample from El Sidrón (Asturias, Spain): How much musculoskeletal variability did Neanderthals accumulate?.}, journal = {Journal of human evolution}, volume = {141}, number = {}, pages = {102746}, doi = {10.1016/j.jhevol.2020.102746}, pmid = {32163763}, issn = {1095-8606}, mesh = {Animals ; Female ; Lower Extremity/growth &amp; development/*physiology ; Male ; Muscle, Skeletal/*growth &amp; development ; *Musculoskeletal Development ; Neanderthals/growth &amp; development/*physiology ; Spain ; }, abstract = {Entheses have rarely been systematically studied in the field of human evolution. However, the investigation of their morphological variability (e.g., robusticity) could provide new insight into their evolutionary significance in the European Neanderthal populations. The aim of this work is to study the entheses and joint features of the lower limbs of El Sidrón Neanderthals (Spain; 49 ka), using standardized scoring methods developed on modern samples. Paleobiology, growth, and development of both juveniles and adults from El Sidrón are studied and compared with those of Krapina Neanderthals (Croatia, 130 ka) and extant humans. The morphological patterns of the gluteus maximus and vastus intermedius entheses in El Sidrón, Krapina, and modern humans differ from one another. Both Neanderthal groups show a definite enthesis design for the gluteus maximus, with little intrapopulation variability with respect to modern humans, who are characterized by a wider range of morphological variability. The gluteus maximus enthesis in the El Sidrón sample shows the osseous features of fibrous entheses, as in modern humans, whereas the Krapina sample shows the aspects of fibrocartilaginous ones. The morphology and anatomical pattern of this enthesis has already been established during growth in all three human groups. One of two and three of five adult femurs from El Sidrón and from Krapina, respectively, show the imprint of the vastus intermedius, which is absent among juveniles from those Neanderthal samples and in modern samples. The scant intrapopulation and the high interpopulation variability in the two Neanderthal samples is likely due to a long-term history of small, isolated populations with high levels of inbreeding, who also lived in different ecological conditions. The comparison of different anatomical entheseal patterns (fibrous vs. fibrocartilaginous) in the Neanderthals and modern humans provides additional elements in the discussion of their functional and genetic origin.}, }
@article {pmid32146203, year = {2020}, author = {Rosas, A and Losada Agustina, B and García-Martínez, D and Torres-Tamayo, N and García-Tabernero, A and Pastor, JF and Rasilla, M and Bastir, M}, title = {Analyses of the neandertal patellae from El Sidrón (Asturias, Spain) with implications for the evolution of body form in Homo.}, journal = {Journal of human evolution}, volume = {141}, number = {}, pages = {102738}, doi = {10.1016/j.jhevol.2019.102738}, pmid = {32146203}, issn = {1095-8606}, mesh = {Animals ; *Biological Evolution ; Fossils/*anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Patella/*anatomy &amp; histology ; *Somatotypes ; Spain ; }, abstract = {The evolution of the body form in Homo and its potential morphological connection to the arrangement of different skeletal systems is of major interest in human evolution. Patella morphology as part of the knee is potentially influenced by body form. Here, we describe for the first time the patellae remains recovered at El Sidrón Neandertal site and analyze them in a comparative evolutionary framework. We aim to clarify whether morphometric features frequently observed in Neandertal and modern human patellae are retained from a primitive anatomical arrangement or whether they represent derived features (apomorphies). For this purpose, we combine analyses of discrete features, classic anthropological measurements, and 3D geometric morphometrics based on generalized Procrustes analysis, mean size and shape comparisons, and principal components analysis. We found a size increment of the patella in hominin evolution, with large species showing a larger patella. Modern humans and Neandertals exhibit overall larger patellae, with maximum values observed in the latter, likely as a consequence of their broader body shape. Also, some Neandertals display a thicker patella, which has been linked to larger quadriceps muscles. However, Neandertals retain a primitive morphology in their patellar articular surfaces, with similar-sized lateral and medial articular facets, leading to a more symmetrical internal face. This feature is inherited from a primitive Homo ancestor and suggests a different configuration of the knee in Neandertals. Conversely, Homo sapiens exhibits an autoapomorphic patellar anatomy with expanded lateral articular facets. We propose that these distinct configurations of the patella within Homo may be a consequence of different body forms rather than specific functional adaptations of the knee. Thus, the slender body form of modern humans may entail a medial reorientation of the tibial tuberosity (patellar ligament), allowing lateral surface expansion. These anatomical evolutionary variations may involve subtle secondary differences in bipedalism within Homo.}, }
@article {pmid32132541, year = {2020}, author = {Gokhman, D and Nissim-Rafinia, M and Agranat-Tamir, L and Housman, G and García-Pérez, R and Lizano, E and Cheronet, O and Mallick, S and Nieves-Colón, MA and Li, H and Alpaslan-Roodenberg, S and Novak, M and Gu, H and Osinski, JM and Ferrando-Bernal, M and Gelabert, P and Lipende, I and Mjungu, D and Kondova, I and Bontrop, R and Kullmer, O and Weber, G and Shahar, T and Dvir-Ginzberg, M and Faerman, M and Quillen, EE and Meissner, A and Lahav, Y and Kandel, L and Liebergall, M and Prada, ME and Vidal, JM and Gronostajski, RM and Stone, AC and Yakir, B and Lalueza-Fox, C and Pinhasi, R and Reich, D and Marques-Bonet, T and Meshorer, E and Carmel, L}, title = {Differential DNA methylation of vocal and facial anatomy genes in modern humans.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1189}, pmid = {32132541}, issn = {2041-1723}, support = {P51 OD011133/OD/NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Aged ; Animals ; Cells, Cultured ; Child ; Chondrocytes ; *DNA Methylation ; *DNA, Ancient ; Evolution, Molecular ; Face/*anatomy &amp; histology ; Female ; Gene Regulatory Networks ; Genetic Speciation ; Humans ; Larynx/anatomy &amp; histology ; Male ; Middle Aged ; Neanderthals/genetics ; Pan troglodytes/genetics ; *Phenotype ; Phonation/*genetics ; Primary Cell Culture ; Tongue/anatomy &amp; histology ; Vocal Cords/anatomy &amp; histology ; Vocalization, Animal ; }, abstract = {Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.}, }
@article {pmid32128408, year = {2020}, author = {Rogers, AR and Harris, NS and Achenbach, AA}, title = {Neanderthal-Denisovan ancestors interbred with a distantly related hominin.}, journal = {Science advances}, volume = {6}, number = {8}, pages = {eaay5483}, pmid = {32128408}, issn = {2375-2548}, mesh = {Animals ; Confidence Intervals ; *Consanguinity ; Gene Flow ; Genetics, Population ; Hominidae/*genetics ; Models, Genetic ; Neanderthals/*genetics ; Phylogeny ; }, abstract = {Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors-members of a "superarchaic" population that separated from other humans about 2 million years ago. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that (i) Denisovans also interbred with superarchaics, (ii) Neanderthals and Denisovans separated early in the middle Pleistocene, (iii) their ancestors endured a bottleneck of population size, and (iv) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (v) Neanderthals interbred with the ancestors of modern humans.}, }
@article {pmid32099103, year = {2020}, author = {Willson, J}, title = {There and back again - ancient genes reveal early migrations.}, journal = {Nature reviews. Genetics}, volume = {21}, number = {4}, pages = {205}, pmid = {32099103}, issn = {1471-0064}, mesh = {DNA, Mitochondrial ; Human Migration ; Humans ; *Neanderthals ; }, }
@article {pmid32095519, year = {2020}, author = {Durvasula, A and Sankararaman, S}, title = {Recovering signals of ghost archaic introgression in African populations.}, journal = {Science advances}, volume = {6}, number = {7}, pages = {eaax5097}, pmid = {32095519}, issn = {2375-2548}, support = {R35 GM125055/GM/NIGMS NIH HHS/United States ; R00 GM111744/GM/NIGMS NIH HHS/United States ; }, mesh = {Blacks/*genetics ; Ethnicity/genetics ; Gene Frequency ; *Genetics, Population ; Humans ; Phylogeny ; }, abstract = {While introgression from Neanderthals and Denisovans has been documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations.}, }
@article {pmid32078934, year = {2020}, author = {Moncel, MH and Ashton, N and Arzarello, M and Fontana, F and Lamotte, A and Scott, B and Muttillo, B and Berruti, G and Nenzioni, G and Tuffreau, A and Peretto, C}, title = {Early Levallois core technology between Marine Isotope Stage 12 and 9 in Western Europe.}, journal = {Journal of human evolution}, volume = {139}, number = {}, pages = {102735}, doi = {10.1016/j.jhevol.2019.102735}, pmid = {32078934}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; *Biological Evolution ; France ; *Hominidae ; Italy ; Neanderthals ; *Technology ; United Kingdom ; }, abstract = {Early Levallois core technology is usually dated in Europe to the end of Marine Isotope Stage (MIS) 9 and particularly from the beginning of MIS 8 to MIS 6. This technology is considered as one of the markers of the transition from lower to Middle Paleolithic or from Mode 2 to Mode 3. Recent discoveries show that some lithic innovations actually appeared earlier in western Europe, from MIS 12 to MIS 9, contemporaneous with changes in subsistence strategies and the first appearance of early Neanderthal anatomical features. Among these discoveries, there is the iconic Levallois core technology. A selection of well-dated assemblages in the United Kingdom, France, and Italy dated from MIS 12 to 9, which include both cores and flakes with Levallois features, has been described and compared with the aim of characterizing this technology. The conclusion supports the interpretation that several technical features may be attributed to a Levallois technology similar to those observed in younger Middle Paleolithic sites, distinct from the main associated core technologies in each level. Some features in the sample of sites suggest a gradual transformation of existing core technologies. The small evidence of Levallois could indicate occasional local innovations from different technological backgrounds and would explain the diversity of Levallois methods that is observed from MIS 12. The technological roots of Levallois technology in the Middle Pleistocene would suggest a multiregional origin and diffusion in Europe and early evidence of regionalization of local traditions through Europe from MIS 12 to 9. The relationships of Levallois technology with new needs and behaviors are discussed, such as flake preference, functional reasons related to hunting and hafting, an increase in the use of mental templates in European populations, and changes in the structure of hominin groups adapting to climatic and environmental changes.}, }
@article {pmid32062432, year = {2020}, author = {Weissbrod, L and Weinstein-Evron, M}, title = {Climate variability in early expansions of Homo sapiens in light of the new record of micromammals in Misliya Cave, Israel.}, journal = {Journal of human evolution}, volume = {139}, number = {}, pages = {102741}, doi = {10.1016/j.jhevol.2020.102741}, pmid = {32062432}, issn = {1095-8606}, mesh = {Animals ; *Biological Evolution ; Caves ; *Climate ; Climate Change ; Fossils ; *Human Migration ; Humans ; Israel ; Mammals ; Neanderthals ; }, abstract = {In this study, we provide the first taphonomic and taxonomic descriptions of the micromammals from Misliya Cave, where recently a Homo sapiens hemimaxilla has been reported. This finding significantly extends the time frame for the out-of-Africa presence of anatomically modern humans. It also provides an opportunity to reassess variation in early modern human population responses to climate change in the Levantine sequence. Information on species ranking and diversity estimations (Shannon functions) is obtained from quantitative data across 31 Levantine assemblages and investigated in a broad comparative frame using multivariate analyses. Recent models of human-climate interactions in the late Early-Middle Paleolithic of the southern Levant have drawn heavily on on-site associations of human fossils with remains of micromammals. However, there has been little, if any, attempt to examine the long-term picture of how paleocommunities of micromammals responded qualitatively and quantitatively to climatic oscillations of the region by altering their compositional complexity. Consequently, our understanding is vastly limited in regard to the paleoecosystem functions that linked past precipitation shifts to changes in primary producers and consumers or as to the background climatic conditions that allowed for the development of highly nonanalog ancient communities in the region. Although previous studies argued for a correspondence between alternations in H. sapiens and Neanderthal occupations of the Levant and faunal shifts in key biostratigraphic indicator taxa (such as Euro-Siberian Ellobius versus Saharo-Arabian Mastomys and Arvicanthis), our data indicate the likelihood that early H. sapiens populations (Misliya and Qafzeh hominins) persisted through high amplitudes of paleoecological and climatic oscillations. It is unlikely, given these results, that climate functioned as a significant filter of early modern human persistence and genetic interactions with Neanderthals in the Levant.}, }
@article {pmid32062431, year = {2020}, author = {Meignen, L and Bar-Yosef, O}, title = {Acheulo-Yabrudian and Early Middle Paleolithic at Hayonim Cave (Western Galilee, Israel): Continuity or break?.}, journal = {Journal of human evolution}, volume = {139}, number = {}, pages = {102733}, doi = {10.1016/j.jhevol.2019.102733}, pmid = {32062431}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; *Biological Evolution ; Caves ; *Hominidae ; Israel ; Neanderthals ; *Technology ; }, abstract = {The long archeological sequence exposed during our renewed excavations in Hayonim Cave sheds new light on the striking technological changes observed at the boundary between the Acheulo-Yabrudian (end of the Lower Paleolithic) and Early Middle Paleolithic in the Levant, as well as on their meaning in terms of population movements. The recent, as yet unpublished, technological studies highlight a clear technological break between these two entities. In Hayonim, the Acheulo-Yabrudian assemblages found at the bottom of the archeological sequence display the specific combination of bifacial shaping and the production of thick, often cortical, flakes frequently shaped into scrapers by Quina retouch. Neither of these lithic production systems is observed in the succeeding Levantine Middle Paleolithic assemblages. In contrast, the Early Middle Paleolithic is characterized by the expansion and diversification of the Levallois production system in its full-fledged form, the emergence of a specific Laminar technology, and a high proportion of retouched tools made on elongated blanks (points and blades). These technological features are unknown in the previous Acheulo-Yabrudian assemblages in the cave. Based on this information, we attempt to determine if the observed changes in stone tool production strategies resulted from an autochthonous development or a dispersal out of Africa.}, }
@article {pmid32047045, year = {2020}, author = {Schmidt, P and Rageot, M and Blessing, M and Tennie, C}, title = {The Zandmotor data do not resolve the question whether Middle Paleolithic birch tar making was complex or not.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {9}, pages = {4456-4457}, pmid = {32047045}, issn = {1091-6490}, mesh = {Archaeology ; Betula ; Humans ; *Neanderthals ; North Sea ; Technology ; }, }
@article {pmid32047044, year = {2020}, author = {Kozowyk, PRB and Langejans, GHJ and Dusseldorp, GL and Niekus, MJLT}, title = {Reply to Schmidt et al.: Interpretation of Paleolithic adhesive production: Combining experimental and paleoenvironmental information.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {9}, pages = {4458-4459}, pmid = {32047044}, issn = {1091-6490}, mesh = {Adhesives ; Archaeology ; *Neanderthals ; North Sea ; Technology ; }, }
@article {pmid32031468, year = {2020}, author = {Le Tortorec, A and Matusali, G and Mahé, D and Aubry, F and Mazaud-Guittot, S and Houzet, L and Dejucq-Rainsford, N}, title = {From Ancient to Emerging Infections: The Odyssey of Viruses in the Male Genital Tract.}, journal = {Physiological reviews}, volume = {100}, number = {3}, pages = {1349-1414}, doi = {10.1152/physrev.00021.2019}, pmid = {32031468}, issn = {1522-1210}, mesh = {Communicable Diseases, Emerging/*virology ; Genitalia, Male/*virology ; Humans ; Male ; Virus Diseases/pathology/*virology ; }, abstract = {The male genital tract (MGT) is the target of a number of viral infections that can have deleterious consequences at the individual, offspring, and population levels. These consequences include infertility, cancers of male organs, transmission to the embryo/fetal development abnormalities, and sexual dissemination of major viral pathogens such as human immunodeficiency virus (HIV) and hepatitis B virus. Lately, two emerging viruses, Zika and Ebola, have additionally revealed that the human MGT can constitute a reservoir for viruses cleared from peripheral circulation by the immune system, leading to their sexual transmission by cured men. This represents a concern for future epidemics and further underlines the need for a better understanding of the interplay between viruses and the MGT. We review here how viruses, from ancient viruses that integrated the germline during evolution through old viruses (e.g., papillomaviruses originating from Neanderthals) and more modern sexually transmitted infections (e.g., simian zoonotic HIV) to emerging viruses (e.g., Ebola and Zika) take advantage of genital tract colonization for horizontal dissemination, viral persistence, vertical transmission, and endogenization. The MGT immune responses to viruses and the impact of these infections are discussed. We summarize the latest data regarding the sources of viruses in semen and the complex role of this body fluid in sexual transmission. Finally, we introduce key animal findings that are relevant for our understanding of viral infection and persistence in the human MGT and suggest future research directions.}, }
@article {pmid32008870, year = {2020}, author = {Wilkins, AS}, title = {A Molecular Investigation of Human Self-Domestication.}, journal = {Trends in genetics : TIG}, volume = {36}, number = {4}, pages = {227-228}, doi = {10.1016/j.tig.2020.01.002}, pmid = {32008870}, issn = {0168-9525}, mesh = {Animals ; Behavior/*physiology ; *Domestication ; Genome, Human/*genetics ; Humans ; Neanderthals/*genetics/physiology ; Transcription Factors/genetics ; }, abstract = {The question of whether human beings are like domesticated animals in their behavior has been simultaneously intriguing, hard to define precisely, and seemingly resistant to any kind of scientific test. A recent paper by Zanella et al. reports a molecular-genetic approach to it and provides a provisional 'yes'.}, }
@article {pmid34692055, year = {2020}, author = {,  and He, Y and Lou, H and Cui, C and Deng, L and Gao, Y and Zheng, W and Guo, Y and Wang, X and Ning, Z and Li, J and Li, B and Bai, C and ,  and ,  and ,  and ,  and ,  and Liu, S and Wu, T and Xu, S and Qi, X and Su, B}, title = {De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation.}, journal = {National science review}, volume = {7}, number = {2}, pages = {391-402}, pmid = {34692055}, issn = {2053-714X}, abstract = {Structural variants (SVs) may play important roles in human adaptation to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome (ZF1), with a contig N50 length of 24.57 mega-base pairs (Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps (0.25 Mb in total length) in the reference human genome (GRCh38). Markedly, we detected 17 900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high-quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid (Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1 (1.32%-1.53%) compared to other East Asian genomes (0.70%-0.98%), reflecting a unique genomic composition of Tibetans. One such archaic hominid shared sequence-a 662-bp intronic insertion in the SCUBE2 gene-is enriched and associated with better lung function (the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies.}, }
@article {pmid32004458, year = {2020}, author = {Chen, L and Wolf, AB and Fu, W and Li, L and Akey, JM}, title = {Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals.}, journal = {Cell}, volume = {180}, number = {4}, pages = {677-687.e16}, doi = {10.1016/j.cell.2020.01.012}, pmid = {32004458}, issn = {1097-4172}, support = {R01 GM110068/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Blacks/*genetics ; *Evolution, Molecular ; Gene Flow ; Human Migration ; Humans ; Models, Genetic ; Neanderthals/*genetics ; Pedigree ; Polymorphism, Genetic ; }, abstract = {Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.}, }
@article {pmid32001636, year = {2020}, author = {Price, M}, title = {Africans, too, carry Neanderthal genetic legacy.}, journal = {Science (New York, N.Y.)}, volume = {367}, number = {6477}, pages = {497}, doi = {10.1126/science.367.6477.497}, pmid = {32001636}, issn = {1095-9203}, mesh = {Africa ; Animals ; Blacks/*genetics ; Europe ; Fossils ; *Gene Flow ; Humans ; Neanderthals/*genetics ; }, }
@article {pmid31988114, year = {2020}, author = {Kolobova, KA and Roberts, RG and Chabai, VP and Jacobs, Z and Krajcarz, MT and Shalagina, AV and Krivoshapkin, AI and Li, B and Uthmeier, T and Markin, SV and Morley, MW and O'Gorman, K and Rudaya, NA and Talamo, S and Viola, B and Derevianko, AP}, title = {Archaeological evidence for two separate dispersals of Neanderthals into southern Siberia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {6}, pages = {2879-2885}, pmid = {31988114}, issn = {1091-6490}, mesh = {Animals ; *Archaeology ; Caves ; Fossils/history ; History, Ancient ; Neanderthals/*genetics ; Siberia ; }, abstract = {Neanderthals were once widespread across Europe and western Asia. They also penetrated into the Altai Mountains of southern Siberia, but the geographical origin of these populations and the timing of their dispersal have remained elusive. Here we describe an archaeological assemblage from Chagyrskaya Cave, situated in the Altai foothills, where around 90,000 Middle Paleolithic artifacts and 74 Neanderthal remains have been recovered from deposits dating to between 59 and 49 thousand years ago (age range at 95.4% probability). Environmental reconstructions suggest that the Chagyrskaya hominins were adapted to the dry steppe and hunted bison. Their distinctive toolkit closely resembles Micoquian assemblages from central and eastern Europe, including the northern Caucasus, more than 3,000 kilometers to the west of Chagyrskaya Cave. At other Altai sites, evidence of earlier Neanderthal populations lacking associated Micoquian-like artifacts implies two or more Neanderthal incursions into this region. We identify eastern Europe as the most probable ancestral source region for the Chagyrskaya toolmakers, supported by DNA results linking the Neanderthal remains with populations in northern Croatia and the northern Caucasus, and providing a rare example of a long-distance, intercontinental population movement associated with a distinctive Paleolithic toolkit.}, }
@article {pmid31975170, year = {2020}, author = {Hubisz, M and Siepel, A}, title = {Inference of Ancestral Recombination Graphs Using ARGweaver.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2090}, number = {}, pages = {231-266}, pmid = {31975170}, issn = {1940-6029}, mesh = {Algorithms ; Animals ; Computational Biology/*methods ; Genetics, Population ; Markov Chains ; Models, Genetic ; Mutation ; Neanderthals/*genetics ; *Recombination, Genetic ; Selection, Genetic ; }, abstract = {This chapter describes the usage of the program ARGweaver, which estimates the ancestral recombination graph for as many as about 100 genome sequences. The ancestral recombination graph is a detailed description of the coalescence and recombination events that define the relationships among the sampled sequences. This rich description is useful for a wide variety of population genetic analyses. We describe the preparation of data and major considerations for running ARGweaver, as well as the interpretation of results. We then demonstrate an analysis using the DARC (Duffy) gene as an example, and show how ARGweaver can be used to detect signatures of natural selection and Neandertal introgression, as well as to estimate the dates of mutation events. This chapter provides sufficient detail to get a new user up and running with this complex but powerful analysis tool.}, }
@article {pmid31940356, year = {2020}, author = {Villa, P and Soriano, S and Pollarolo, L and Smriglio, C and Gaeta, M and D'Orazio, M and Conforti, J and Tozzi, C}, title = {Neandertals on the beach: Use of marine resources at Grotta dei Moscerini (Latium, Italy).}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0226690}, pmid = {31940356}, issn = {1932-6203}, mesh = {Animal Shells ; Animals ; *Aquatic Organisms ; Archaeology ; Bivalvia/anatomy &amp; histology ; Italy ; *Neanderthals ; Silicates ; *Tool Use Behavior ; }, abstract = {Excavated in 1949, Grotta dei Moscerini, dated MIS 5 to early MIS 4, is one of two Italian Neandertal sites with a large assemblage of retouched shells (n = 171) from 21 layers. The other occurrence is from the broadly contemporaneous layer L of Grotta del Cavallo in southern Italy (n = 126). Eight other Mousterian sites in Italy and one in Greece also have shell tools but in a very small number. The shell tools are made on valves of the smooth clam Callista chione. The general idea that the valves of Callista chione were collected by Neandertals on the beach after the death of the mollusk is incomplete. At Moscerini 23.9% of the specimens were gathered directly from the sea floor as live animals by skin diving Neandertals. Archaeological data from sites in Italy, France and Spain confirm that shell fishing and fresh water fishing was a common activity of Neandertals, as indicated by anatomical studies recently published by E. Trinkaus. Lithic analysis provides data to show the relation between stone tools and shell tools. Several layers contain pumices derived from volcanic eruptions in the Ischia Island or the Campi Flegrei (prior to the Campanian Ignimbrite mega-eruption). Their rounded edges indicate that they were transported by sea currents to the beach at the base of the Moscerini sequence. Their presence in the occupation layers above the beach is discussed. The most plausible hypothesis is that they were collected by Neandertals. Incontrovertible evidence that Neandertals collected pumices is provided by a cave in Liguria. Use of pumices as abraders is well documented in the Upper Paleolithic. We prove that the exploitation of submerged aquatic resources and the collection of pumices common in the Upper Paleolithic were part of Neandertal behavior well before the arrival of modern humans in Western Europe.}, }
@article {pmid31935281, year = {2020}, author = {Gouy, A and Excoffier, L}, title = {Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens.}, journal = {Molecular biology and evolution}, volume = {37}, number = {5}, pages = {1420-1433}, doi = {10.1093/molbev/msz306}, pmid = {31935281}, issn = {1537-1719}, mesh = {Adaptation, Biological/*genetics ; *Genetic Introgression ; Host-Pathogen Interactions/*genetics ; Humans ; Melanesia ; *Multifactorial Inheritance ; *Selection, Genetic ; }, abstract = {Anatomically modern humans carry many introgressed variants from other hominins in their genomes. Some of them affect their phenotype and can thus be negatively or positively selected. Several individual genes have been proposed to be the subject of adaptive introgression, but the possibility of polygenic adaptive introgression has not been extensively investigated yet. In this study, we analyze archaic introgression maps with refined functional enrichment methods to find signals of polygenic adaptation of introgressed variants. We first apply a method to detect sets of connected genes (subnetworks) within biological pathways that present higher-than-expected levels of archaic introgression. We then introduce and apply a new statistical test to distinguish between epistatic and independent selection in gene sets of present-day humans. We identify several known targets of adaptive introgression, and we show that they belong to larger networks of introgressed genes. After correction for genetic linkage, we find that signals of polygenic adaptation are mostly explained by independent and potentially sequential selection episodes. However, we also find some gene sets where introgressed variants present significant signals of epistatic selection. Our results confirm that archaic introgression has facilitated local adaptation, especially in immunity related and metabolic functions and highlight its involvement in a coordinated response to pathogens out of Africa.}, }
@article {pmid31898502, year = {2020}, author = {Rotival, M and Quintana-Murci, L}, title = {Functional consequences of archaic introgression and their impact on fitness.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {3}, pmid = {31898502}, issn = {1474-760X}, mesh = {Adaptation, Biological ; Alleles ; Animals ; Epistasis, Genetic ; *Genetic Fitness ; *Genetic Introgression ; *Genome, Human ; Haplotypes ; Humans ; Neanderthals/*genetics ; }, }
@article {pmid31889305, year = {2020}, author = {Gómez-Olivencia, A and López-Onaindia, D and Sala, N and Balzeau, A and Pantoja-Pérez, A and Arganda-Carreras, I and Arlegi, M and Rios-Garaizar, J and Gómez-Robles, A}, title = {The human remains from Axlor (Dima, Biscay, northern Iberian Peninsula).}, journal = {American journal of physical anthropology}, volume = {172}, number = {3}, pages = {475-491}, doi = {10.1002/ajpa.23989}, pmid = {31889305}, issn = {1096-8644}, mesh = {Adult ; Animals ; Anthropology, Physical ; Child ; *Fossils ; History, Ancient ; Humans ; Neanderthals ; Skull/*anatomy &amp; histology ; Spain ; Tooth/*anatomy &amp; histology ; }, abstract = {OBJECTIVES: We provide the description and comparative analysis of all the human fossil remains found at Axlor during the excavations carried out by J. M. de Barandiarán from 1967 to 1974: a cranial vault fragment and seven teeth, five of which likely belonged to the same individual, although two are currently lost. Our goal is to describe in detail all these human remains and discuss both their taxonomic attribution and their stratigraphic context.<br><br>MATERIALS AND METHODS: We describe external and internal anatomy, and use classic and geometric morphometrics. The teeth from Axlor are compared to Neandertals, Upper Paleolithic, and recent modern humans.<br><br>RESULTS: Two teeth (a left dm[2] , a left di[1]) and the parietal fragment show morphological features consistent with a Neandertal classification, and were found in an undisturbed Mousterian context. The remaining three teeth (plus the two lost ones), initially classified as Neandertals, show morphological features and a general size that are more compatible with their classification as modern humans.<br><br>DISCUSSION: A left parietal fragment (Level VIII) from a single probably adult Neandertal individual was recovered during the old excavations performed by Barandiar&#xe1;n. Additionally, two different Neandertal children lost deciduous teeth during the formations of levels V (left di[1]) and IV (right dm[2]). In addition, a modern human individual is represented by five remains (two currently lost) from a complex stratigraphic setting. Some of the morphological features of these remains suggest that they may represent one of the scarce examples of Upper Paleolithic modern human remains in the northern Iberian Peninsula, which should be confirmed by direct dating.}, }
@article {pmid31878873, year = {2019}, author = {Bücking, R and Cox, MP and Hudjashov, G and Saag, L and Sudoyo, H and Stoneking, M}, title = {Archaic mitochondrial DNA inserts in modern day nuclear genomes.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {1017}, pmid = {31878873}, issn = {1471-2164}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genomics/*methods ; Hominidae/genetics ; Neanderthals/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs).<br><br>RESULTS: We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male.<br><br>CONCLUSIONS: Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.}, }
@article {pmid31878147, year = {2019}, author = {Batyrev, D and Lapid, E and Carmel, L and Meshorer, E}, title = {Predicted Archaic 3D Genome Organization Reveals Genes Related to Head and Spinal Cord Separating Modern from Archaic Humans.}, journal = {Cells}, volume = {9}, number = {1}, pages = {}, pmid = {31878147}, issn = {2073-4409}, support = {1140/17//Israel Science Foundation/International ; }, mesh = {Animals ; DNA Methylation/genetics ; DNA, Ancient/analysis ; Databases, Genetic ; Epigenesis, Genetic/genetics ; Genome/genetics ; Genomics/methods ; Head/*anatomy &amp; histology ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; Promoter Regions, Genetic/genetics ; Spinal Cord/*anatomy &amp; histology ; }, abstract = {High coverage sequences of archaic humans enabled the reconstruction of their DNA methylation patterns. This allowed comparing gene regulation between human groups, and linking such regulatory changes to phenotypic differences. In a previous work, a detailed comparison of DNA methylation in modern humans, archaic humans, and chimpanzees revealed 873 modern human-derived differentially methylated regions (DMRs). To understand the regulatory implications of these DMRs, we defined differentially methylated genes (DMGs) as genes that harbor DMRs in their promoter or gene body. While most of the modern human-derived DMRs could be linked to DMGs, many others remained unassigned. Here, we used information on 3D genome organization to link ~70 out of the remaining 288 unassigned DMRs to genes. Combined with the previously identified DMGs, we reinforce the enrichment of these genes with vocal and facial anatomy, and additionally find significant enrichment with the spinal column, chin, hair, and scalp. These results reveal the importance of 3D genomic organization in understanding gene regulation by DNA methylation.}, }
@article {pmid31873124, year = {2019}, author = {Ottoni, C and Guellil, M and Ozga, AT and Stone, AC and Kersten, O and Bramanti, B and Porcier, S and Van Neer, W}, title = {Metagenomic analysis of dental calculus in ancient Egyptian baboons.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19637}, pmid = {31873124}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient/*analysis ; Dental Calculus/*microbiology ; Egypt ; Humans ; *Metagenome ; Microbiota/*genetics ; Neanderthals ; Pan troglodytes ; Papio ; }, abstract = {Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals' oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9[th]-6[th] centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons' oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.}, }
@article {pmid31809748, year = {2019}, author = {Wall, JD and Ratan, A and Stawiski, E and , }, title = {Identification of African-Specific Admixture between Modern and Archaic Humans.}, journal = {American journal of human genetics}, volume = {105}, number = {6}, pages = {1254-1261}, pmid = {31809748}, issn = {1537-6605}, support = {P30 CA044579/CA/NCI NIH HHS/United States ; R01 GM115433/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Blacks/*genetics ; *Fossils ; Gene Pool ; *Genetics, Population ; *Genome, Human ; Hominidae/*genetics ; Humans ; Neanderthals/*genetics ; }, abstract = {Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.}, }
@article {pmid31802585, year = {2020}, author = {Langley, MC and Benítez-Burraco, A and Kempe, V}, title = {Playing with language, creating complexity: Has play contributed to the evolution of complex language?.}, journal = {Evolutionary anthropology}, volume = {29}, number = {1}, pages = {29-40}, doi = {10.1002/evan.21810}, pmid = {31802585}, issn = {1520-6505}, mesh = {Animals ; Behavior, Animal ; Child ; Child Behavior/*ethnology ; *Cultural Evolution ; History, Ancient ; Humans ; Language/*history ; Neanderthals/physiology ; *Play and Playthings ; }, abstract = {We argue that enhanced play may have contributed to the emergence of complex language systems in modern humans (Homo sapiens). To support this idea, we first discuss evidence for an expansion of playing behavior connected to the extended childhood of modern human children, and the potential of this period for the transmission of complex cultural traits, including language. We then link two of the most important functions of play-exploration and innovation-to the potential for cumulative cultural evolution in general and for the emergence of complex language in particular. If correct, the shorter childhood of Neanderthals-involving restrictions on time to experiment and innovate-may have restricted their language (and other symbolic) system/s. Consequently, fully investigating the role that play may have had in the transmission of language and the development of symbolic cultures in both modern humans and Neanderthals provides a new avenue of research for Paleolithic archaeology and related disciplines.}, }
@article {pmid31800577, year = {2019}, author = {Weniger, GC and de Andrés-Herrero, M and Bolin, V and Kehl, M and Otto, T and Potì, A and Tafelmaier, Y}, title = {Late Glacial rapid climate change and human response in the Westernmost Mediterranean (Iberia and Morocco).}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225049}, pmid = {31800577}, issn = {1932-6203}, mesh = {*Agriculture ; *Climate Change ; Human Migration ; Humans ; Mediterranean Region ; Radiometric Dating ; Soil/chemistry ; }, abstract = {This paper investigates the correlation between climate, environment and human land use in the Westernmost Mediterranean on both sides of the Strait of Gibraltar during the Late Glacial. Using a multi-proxy approach on a sample of 300 sites from the Solutrean and Magdalenian of the Iberian Peninsula and from the Iberomaurusian in Morocco, we find evidence for significant changes in settlement patterns and site density after the Last Glacial Maximum. In Southern Iberia, during Heinrich Stadial 1, hyperarid zones expanded drastically from the south-eastern coast to the West through the Interior. This aridification process heavily affected Magdalenian settlement in the South and caused a strong decline of hunter-gatherer population. Southern Iberia during Heinrich Stadial 1 turned out to be a high-risk environment when compared to Northern Iberia. At the same time, the Late Iberomaurusian of Morocco, although considered to be situated in a high-risk environment as well, experiences an increase of sites and expansion of settlement area.}, }
@article {pmid31797875, year = {2019}, author = {Mallol, C and Hernández, C and Mercier, N and Falguères, C and Carrancho, &#xc1; and Cabanes, D and Vidal-Matutano, P and Connolly, R and Pérez, L and Mayor, A and Ben Arous, E and Galván, B}, title = {Fire and brief human occupations in Iberia during MIS 4: Evidence from Abric del Pastor (Alcoy, Spain).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18281}, pmid = {31797875}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Caves ; *Fires ; *Fossils ; Humans ; *Neanderthals ; Radiometric Dating ; Spain ; }, abstract = {There is a relatively low amount of Middle Paleolithic sites in Europe dating to MIS 4. Of the few that exist, several of them lack evidence for anthropogenic fire, raising the question of how this period of global cooling may have affected the Neanderthal population. The Iberian Peninsula is a key area to explore this issue, as it has been considered as a glacial refugium during critical periods of the Neanderthal timeline and might therefore yield archaeological contexts in which we can explore possible changes in the behaviour and settlement patterns of Neanderthal groups during MIS 4. Here we report recent data from Abric del Pastor, a small rock shelter in Alcoy (Alicante, Spain) with a stratified deposit containing Middle Palaeolithic remains. We present absolute dates that frame the sequence within MIS 4 and multi-proxy geoarchaeological evidence of in situ anthropogenic fire, including microscopic evidence of in situ combustion residues and thermally altered sediment. We also present archaeostratigraphic evidence of recurrent, functionally diverse, brief human occupation of the rock shelter. Our results suggest that Neanderthals occupied the Central Mediterranean coast of the Iberian Peninsula during MIS 4, that these Neanderthals were not undergoing climatic stress and they were habitual fire users.}, }
@article {pmid31797354, year = {2020}, author = {Karban, ME}, title = {Occipital hemi-bun development and shape covariation in a longitudinal extant human growth sample.}, journal = {American journal of physical anthropology}, volume = {172}, number = {1}, pages = {123-134}, doi = {10.1002/ajpa.23981}, pmid = {31797354}, issn = {1096-8644}, mesh = {Adolescent ; Canada ; Child ; Child, Preschool ; Female ; Humans ; Male ; Occipital Bone/*anatomy &amp; histology/growth &amp; development ; United States ; Young Adult ; }, abstract = {OBJECTIVES: Although the homology of the Neanderthal occipital bun and anatomically modern human "hemi-bun" has long been debated, little is known about the developmental timing and patterning of these two patterns of prominent occipital squama convexity. In this study, occipital hemi-bun ontogeny and cranial shape covariation are assessed in a comparative extant human sample.<br><br>MATERIALS AND METHODS: Two-dimensional geometric morphometric methods were used to investigate hemi-bun development in a longitudinal sample of growth study cephalograms representing extant human subjects predominantly of European ancestry. Subjects were each measured at three distinct age points, ranging from 3.0 to 20.4&#x2009;years, and two-block partial least squares analysis was used to assess patterns of covariation between midsagittal occipital bone morphology and other aspects of craniofacial shape.<br><br>RESULTS: Occipital hemi-bun morphology, when present, was found to develop early in ontogeny, in association with anteroposterior elongation of the frontal and parietal bones. No significant pattern of covariation was found between occipital hemi-bun shape and cranial/basicranial breadth, basicranial length, basicranial angle, or midfacial prognathism.<br><br>DISCUSSION: This study suggests that the occipital hemi-bun, at least in this extant human population, should not be considered an independent trait, as its development is closely linked to shape variation in the frontal and parietal bones. Importantly, these results suggest that occipital hemi-bun morphology is not significantly influenced by basicranial morphology during development, but instead covaries with changes in midsagittal neurocranial vault shape.}, }
@article {pmid31774843, year = {2019}, author = {Vaesen, K and Scherjon, F and Hemerik, L and Verpoorte, A}, title = {Inbreeding, Allee effects and stochasticity might be sufficient to account for Neanderthal extinction.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0225117}, pmid = {31774843}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Extinction, Biological ; Female ; Humans ; *Inbreeding ; Models, Biological ; Neanderthals/*physiology ; Stochastic Processes ; }, abstract = {The replacement of Neanderthals by Anatomically Modern Humans has typically been attributed to environmental pressure or a superiority of modern humans with respect to competition for resources. Here we present two independent models that suggest that no such heatedly debated factors might be needed to account for the demise of Neanderthals. Starting from the observation that Neanderthal populations already were small before the arrival of modern humans, the models implement three factors that conservation biology identifies as critical for a small population's persistence, namely inbreeding, Allee effects and stochasticity. Our results indicate that the disappearance of Neanderthals might have resided in the smallness of their population(s) alone: even if they had been identical to modern humans in their cognitive, social and cultural traits, and even in the absence of inter-specific competition, Neanderthals faced a considerable risk of extinction. Furthermore, we suggest that if modern humans contributed to the demise of Neanderthals, that contribution might have had nothing to do with resource competition, but rather with how the incoming populations geographically restructured the resident populations, in a way that reinforced Allee effects, and the effects of inbreeding and stochasticity.}, }
@article {pmid31774826, year = {2019}, author = {Krueger, KL and Willman, JC and Matthews, GJ and Hublin, JJ and Pérez-Pérez, A}, title = {Anterior tooth-use behaviors among early modern humans and Neandertals.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0224573}, pmid = {31774826}, issn = {1932-6203}, mesh = {Animals ; Anthropology, Physical ; Behavior/*physiology ; Biomechanical Phenomena ; Ecosystem ; Fossils/*anatomy &amp; histology ; Humans ; Incisor/*anatomy &amp; histology/diagnostic imaging/physiology ; Mastication/physiology ; Neanderthals/*anatomy &amp; histology/physiology ; Surface Properties ; Tooth Wear/diagnostic imaging/*etiology ; }, abstract = {Early modern humans (EMH) are often touted as behaviorally advanced to Neandertals, with more sophisticated technologies, expanded resource exploitation, and more complex clothing production. However, recent analyses have indicated that Neandertals were more nuanced in their behavioral adaptations, with the production of the Châtelperronian technocomplex, the processing and cooking of plant foods, and differences in behavioral adaptations according to habitat. This study adds to this debate by addressing the behavioral strategies of EMH (n = 30) within the context of non-dietary anterior tooth-use behaviors to glean possible differences between them and their Neandertal (n = 45) counterparts. High-resolution casts of permanent anterior teeth were used to collect microwear textures of fossil and comparative bioarchaeological samples using a Sensofar white-light confocal profiler with a 100x objective lens. Labial surfaces were scanned, totaling a work envelope of 204 x 276 μm for each individual. The microwear textures were examined for post-mortem damage and uploaded to SSFA software packages for surface characterization. Statistical analyses were performed to examine differences in central tendencies and distributions of anisotropy and textural fill volume variables among the EMH sample itself by habitat, location, and time interval, and between the EMH and Neandertal samples by habitat and location. Descriptive statistics for the EMH sample were compared to seven bioarchaeological samples (n = 156) that utilized different tooth-use behaviors to better elucidate specific activities that may have been performed by EMH. Results show no significant differences between the means within the EMH sample by habitat, location, or time interval. Furthermore, there are no significant differences found here between EMH and Neandertals. Comparisons to the bioarchaeological samples suggest both fossil groups participated in clamping and grasping activities. These results indicate that EMH and Neandertals were similar in their non-dietary anterior tooth-use behaviors and provide additional evidence for overlapping behavioral strategies employed by these two hominins.}, }
@article {pmid31765984, year = {2020}, author = {Garralda, MD and Maureille, B and Le Cabec, A and Oxilia, G and Benazzi, S and Skinner, MM and Hublin, JJ and Vandermeersch, B}, title = {The Neanderthal teeth from Marillac (Charente, Southwestern France): Morphology, comparisons and paleobiology.}, journal = {Journal of human evolution}, volume = {138}, number = {}, pages = {102683}, doi = {10.1016/j.jhevol.2019.102683}, pmid = {31765984}, issn = {1095-8606}, support = {724046/ERC_/European Research Council/International ; }, mesh = {Animals ; Archaeology ; Fossils/*anatomy &amp; histology ; France ; Neanderthals/*anatomy &amp; histology ; Tooth/*anatomy &amp; histology ; }, abstract = {Few European sites have yielded human dental remains safely dated to the end of MIS 4/beginning of MIS 3. One of those sites is Marillac (Southwestern France), a collapsed karstic cave where archeological excavations (1967-1980) conducted by B. Vandermeersch unearthed numerous faunal and human remains, as well as a few Mousterian Quina tools. The Marillac sinkhole was occasionally used by humans to process the carcasses of different prey, but there is no evidence for a residential use of the site, nor have any hearths been found. Rare carnivore bones were also discovered, demonstrating that the sinkhole was seasonally used, not only by Neanderthals, but also by predators across several millennia. The lithostratigraphic units containing the human remains were dated to ∼60 kyr. The fossils consisted of numerous fragments of skulls and jaws, isolated teeth and several post-cranial bones, many of them with traces of perimortem manipulations. For those already published, their morphological characteristics and chronostratigraphic context allowed their attribution to Neanderthals. This paper analyzes sixteen unpublished human teeth (fourteen permanent and two deciduous) by investigating the external morphology and metrical variation with respect to other Neanderthal remains and a sample from modern populations. We also investigate their enamel thickness distribution in 2D and 3D, the enamel-dentine junction morphology (using geometric morphometrics) of one molar and two premolars, the roots and the possible expression of taurodontism, as well as pathologies and developmental defects. The anterior tooth use and paramasticatory activities are also discussed. Morphological and structural alterations were found on several teeth, and interpreted in light of human behavior (tooth-pick) and carnivores' actions (partial digestion). The data are interpreted in the context of the available information for the Eurasian Neanderthals.}, }
@article {pmid31733113, year = {2020}, author = {Andrews, P and Johnson, RJ}, title = {Evolutionary basis for the human diet: consequences for human health.}, journal = {Journal of internal medicine}, volume = {287}, number = {3}, pages = {226-237}, doi = {10.1111/joim.13011}, pmid = {31733113}, issn = {1365-2796}, mesh = {Adaptation, Physiological ; Animals ; *Biological Evolution ; Climate ; Diet/*trends ; Ecosystem ; Fossils ; Hominidae ; Humans ; Phenotype ; }, abstract = {The relationship of evolution with diet and environment can provide insights into modern disease. Fossil evidence shows apes, and early human ancestors were fruit eaters living in environments with strongly seasonal climates. Rapid cooling at the end of the Middle Miocene (15-12 Ma: millions of years ago) increased seasonality in Africa and Europe, and ape survival may be linked with a mutation in uric acid metabolism. Climate stabilized in the later Miocene and Pliocene (12-5 Ma), and fossil apes and early hominins were both adapted for life on ground and in trees. Around 2.5 Ma, early species of Homo introduced more animal products into their diet, and this coincided with developing bipedalism, stone tool technology and increase in brain size. Early species of Homo such as Homo habilis still lived in woodland habitats, and the major habitat shift in human evolution occurred at 1.8 Ma with the origin of Homo erectus. Homo erectus had increased body size, greater hunting skills, a diet rich in meat, control of fire and understanding about cooking food, and moved from woodland to savannah. Group size may also have increased at the same time, facilitating the transmission of knowledge from one generation to the next. The earliest fossils of Homo sapiens appeared about 300 kyr, but they had separated from Neanderthals by 480 kyr or earlier. Their diet shifted towards grain-based foods about 100 kyr ago, and settled agriculture developed about 10 kyr ago. This pattern remains for many populations to this day and provides important insights into current burden of lifestyle diseases.}, }
@article {pmid31725722, year = {2019}, author = {V Barroso, G and Puzović, N and Dutheil, JY}, title = {Inference of recombination maps from a single pair of genomes and its application to ancient samples.}, journal = {PLoS genetics}, volume = {15}, number = {11}, pages = {e1008449}, pmid = {31725722}, issn = {1553-7404}, mesh = {Animals ; Chromosome Mapping ; Genetic Variation/genetics ; Genome, Human/*genetics ; Hominidae/*genetics ; Humans ; Markov Chains ; *Metagenomics ; Neanderthals/genetics ; Paleontology/trends ; Phylogeny ; Recombination, Genetic/*genetics ; }, abstract = {Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefore necessary to research organisms where such datasets cannot be generated easily, such as non-model or ancient species. Here we extend the sequentially Markovian coalescent model to jointly infer demography and the spatial variation in recombination rate. Using extensive simulations and sequence data from humans, fruit-flies and a fungal pathogen, we demonstrate that iSMC accurately infers recombination maps under a wide range of scenarios-remarkably, even from a single pair of unphased genomes. We exploit this possibility and reconstruct the recombination maps of ancient hominins. We report that the ancient and modern maps are correlated in a manner that reflects the established phylogeny of Neanderthals, Denisovans, and modern human populations.}, }
@article {pmid31710710, year = {2020}, author = {Rmoutilová, R and Gómez-Olivencia, A and Brůžek, J and Holliday, T and Ledevin, R and Couture-Veschambre, C and Madelaine, S and Džupa, V and Velemínská, J and Maureille, B}, title = {A case of marked bilateral asymmetry in the sacral alae of the Neandertal specimen Regourdou 1 (Périgord, France).}, journal = {American journal of physical anthropology}, volume = {171}, number = {2}, pages = {242-259}, doi = {10.1002/ajpa.23968}, pmid = {31710710}, issn = {1096-8644}, support = {ANR-10-LABX-52//French National Research Agency/International ; 1088217//Agency of Charles University/International ; //Irene Levi Sala CARE Archaeological Foundation/International ; //Leakey Foundation/International ; LEQSF(2015-18)-RD-A-22//Louisiana Board of Regents/International ; PGC2018-093925-B-C33//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/International ; CGL2015-65387-C3-2-P//Ministerio de Econom&#xed;a y Competitividad/International ; 2016-1R40240-00007349-00007350//R&#xe9;gion Nouvelle Aquitaine/International ; 1044-16//Universidad del Pa&#xed;s Vasco/Euskal Herriko Unibertsitatea/International ; IT1418-19//Eusko Jaurlaritza-Gobierno Vasco/International ; }, mesh = {Animals ; Fossils/*anatomy &amp; histology ; France ; Neanderthals/*abnormalities ; Sacrum/*abnormalities ; }, abstract = {OBJECTIVES: A marked asymmetry was previously reported in the sacral alae and S1-L5 facets orientation of the Neandertal individual Regourdou 1. Here, we provide a detailed description and quantification of the morphology and degree of asymmetry of this sacrum.<br><br>MATERIAL AND METHODS: Regourdou 1 was compared to a modern human sample composed of 24 females and 17 males, and to other Neandertal individuals. Both traditional and geometric morphometric analyses were used in order to quantify the degree of sacral asymmetry of Regourdou 1.<br><br>RESULTS: The asymmetry of both sacral alae and facets orientation substantially exceeds directional and absolute asymmetry of the healthy modern sample. Regourdou 1 shows a considerably shorter right ala, which is absolutely and relatively outside of the modern and Neandertal variations.<br><br>CONCLUSION: Regourdou 1 shows marked sacral asymmetry that probably originated in early ontogenetic development. An asymmetric sacrum reflects asymmetric load dissipation and could relate to other morphological abnormalities observed in the skeleton, especially the mild scoliosis of the spine and the asymmetry of the femoral diaphyses. Further investigation is necessary to elucidate the relationship between those morphologies as well as a potential impact on the life of the individual.}, }
@article {pmid31702050, year = {2020}, author = {Gokcumen, O}, title = {Archaic hominin introgression into modern human genomes.}, journal = {American journal of physical anthropology}, volume = {171 Suppl 70}, number = {}, pages = {60-73}, doi = {10.1002/ajpa.23951}, pmid = {31702050}, issn = {1096-8644}, support = {1714867//United States National Science Foundation/International ; }, mesh = {Animals ; DNA/genetics ; *Gene Flow ; *Genetic Introgression ; *Genome, Human ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; }, abstract = {Ancient genomes from multiple Neanderthal and the Denisovan individuals, along with DNA sequence data from diverse contemporary human populations strongly support the prevalence of gene flow among different hominins. Recent studies now provide evidence for multiple gene flow events that leave genetic signatures in extant and ancient human populations. These events include older gene flow from an unknown hominin in Africa predating out-of-Africa migrations, and in the last 50,000-100,000 years, multiple gene flow events from Neanderthals into ancestral Eurasian human populations, and at least three distinct introgression events from a lineage close to Denisovans into ancestors of extant Southeast Asian and Oceanic populations. Some of these introgression events may have happened as late as 20,000 years before present and reshaped the way in which we think about human evolution. In this review, I aim to answer anthropologically relevant questions with regard to recent research on ancient hominin introgression in the human lineage. How have genomic data from archaic hominins changed our view of human evolution? Is there any doubt about whether introgression from ancient hominins to the ancestors of present-day humans occurred? What is the current view of human evolutionary history from the genomics perspective? What is the impact of introgression on human phenotypes?}, }
@article {pmid31701003, year = {2019}, author = {Rodríguez-Hidalgo, A and Morales, JI and Cebrià, A and Courtenay, LA and Fernández-Marchena, JL and García-Argudo, G and Marín, J and Saladié, P and Soto, M and Tejero, JM and Fullola, JM}, title = {The Châtelperronian Neanderthals of Cova Foradada (Calafell, Spain) used imperial eagle phalanges for symbolic purposes.}, journal = {Science advances}, volume = {5}, number = {11}, pages = {eaax1984}, pmid = {31701003}, issn = {2375-2548}, mesh = {Animals ; *Archaeology ; Fossils ; Geography ; Humans ; *Neanderthals ; Spain ; }, abstract = {Evidence for the symbolic behavior of Neanderthals in the use of personal ornaments is relatively scarce. Among the few ornaments documented, eagle talons, which were presumably used as pendants, are the most frequently recorded. This phenomenon appears concentrated in a specific area of southern Europe during a span of 80 thousand years. Here, we present the analysis of one eagle pedal phalange recovered from the Châtelperronian layer of Foradada Cave (Spain). Our research broadens the known geographical and temporal range of this symbolic behavior, providing the first documentation of its use among the Iberian populations, as well as of its oldest use in the peninsula. The recurrent appearance of large raptor talons throughout the Middle Paleolithic time frame, including their presence among the last Neanderthal populations, raises the question of the survival of some cultural elements of the Middle Paleolithic into the transitional Middle to Upper Paleolithic assemblages and beyond.}, }
@article {pmid31676766, year = {2019}, author = {Greenbaum, G and Getz, WM and Rosenberg, NA and Feldman, MW and Hovers, E and Kolodny, O}, title = {Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {5003}, pmid = {31676766}, issn = {2041-1723}, mesh = {Algorithms ; Animals ; Communicable Diseases/*genetics/immunology/transmission ; Fossils ; Geography ; Hominidae/*genetics/immunology ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Models, Genetic ; Neanderthals/*genetics/immunology ; Population Dynamics ; }, abstract = {Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-based transmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated 'pathogen packages' could have generated feedback that allowed modern humans to overcome disease burden earlier than Neanderthals, giving them an advantage in their subsequent spread into Eurasia.}, }
@article {pmid31675491, year = {2019}, author = {Kozowyk, PRB and Poulis, JA}, title = {A new experimental methodology for assessing adhesive properties shows that Neandertals used the most suitable material available.}, journal = {Journal of human evolution}, volume = {137}, number = {}, pages = {102664}, doi = {10.1016/j.jhevol.2019.102664}, pmid = {31675491}, issn = {1095-8606}, mesh = {Adhesives/*chemistry ; Animals ; Archaeology/instrumentation/*methods ; Fossils ; Hardness ; *Neanderthals ; Rheology ; Technology ; Thermogravimetry ; }, abstract = {The use of adhesives for hafting stone tools at least 191 ka was a major technological development. Stone tools could be more securely attached to handles, thus improving their efficiency and practicality. To produce functional adhesives required forethought and planning, as well as expertise and knowledge of the resources available in the landscape. This makes adhesives important in discussions about Neandertal and early modern human technological and mental capabilities. However, we currently know very little about how these early adhesive materials behaved under different circumstances, or why certain materials were used and others were not. Here we present the results of controlled laboratory bulk property tests (hardness, rheology and thermogravimetric analysis) on replica Paleolithic adhesives. We conclude that birch tar is more versatile, has better working properties, and is more reusable than pine resin, the most likely alternative material. Neandertals may therefore have invested more time and resources to produce birch tar because it was the best material available, both functionally and economically, throughout the majority of Europe during the Middle to Late Pleistocene. Our results further demonstrate that Neandertals had high levels of technological expertise and knowledge of the natural resources available to them in their environment.}, }
@article {pmid31669124, year = {2020}, author = {Bataille, G and Falcucci, A and Tafelmaier, Y and Conard, NJ}, title = {Technological differences between Kostenki 17/II (Spitsynskaya industry, Central Russia) and the Protoaurignacian: Reply to Dinnis et al. (2019).}, journal = {Journal of human evolution}, volume = {146}, number = {}, pages = {102685}, doi = {10.1016/j.jhevol.2019.102685}, pmid = {31669124}, issn = {1095-8606}, mesh = {Animals ; *Neanderthals ; Russia ; *Technology ; }, }
@article {pmid31663021, year = {2019}, author = {Carter, T and Contreras, DA and Holcomb, J and Mihailović, DD and Karkanas, P and Guérin, G and Taffin, N and Athanasoulis, D and Lahaye, C}, title = {Earliest occupation of the Central Aegean (Naxos), Greece: Implications for hominin and Homo sapiens' behavior and dispersals.}, journal = {Science advances}, volume = {5}, number = {10}, pages = {eaax0997}, pmid = {31663021}, issn = {2375-2548}, mesh = {Africa ; Animals ; Europe ; Fossils ; Greece ; Hominidae/*genetics ; Neanderthals ; Occupations ; }, abstract = {We present evidence of Middle Pleistocene activity in the central Aegean Basin at the chert extraction and reduction complex of Stelida (Naxos, Greece). Luminescence dating places ~9000 artifacts in a stratigraphic sequence from ~13 to 200 thousand years ago (ka ago). These artifacts include Mousterian products, which arguably provide first evidence for Neanderthals in the region. This dated material attests to a much earlier history of regional exploration than previously believed, opening the possibility of alternative routes into Southeast Europe from Anatolia (and Africa) for (i) hominins, potentially during sea level lowstands (e.g., Marine Isotope Stage 8) permitting terrestrial crossings across the Aegean, and (ii) Homo sapiens of the Early Upper Paleolithic (Aurignacian), conceivably by sea.}, }
@article {pmid31651929, year = {2019}, author = {Abdelhady, AA and Elewa, AMT and El-Dawy, MH}, title = {The position of Neandertal and Homo erectus within the hominid clade based on craniodental morphology and whole mtDNA genomes.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {70}, number = {4}, pages = {303-323}, doi = {10.1127/homo/2019/1119}, pmid = {31651929}, issn = {1618-1301}, mesh = {Animals ; Anthropology, Physical ; Biological Evolution ; DNA, Mitochondrial/genetics ; Female ; *Genome, Mitochondrial/genetics ; *Hominidae/anatomy &amp; histology/classification/genetics ; Humans ; Male ; *Neanderthals/anatomy &amp; histology/classification/genetics ; Phylogeny ; Skull/*anatomy &amp; histology ; Tooth/*anatomy &amp; histology ; }, abstract = {To evaluate the taxonomic position of the Neandertal and Homo erectus within the hominid clade, the variation among and within the hominid taxa was assessed based on the craniodental morphology and integrated with molecular analyses of the whole mtDNA genomes. Ordination and clustering of the Procrustes craniodental landmarks have showed a notable shape transformation from the earliest hominid species to the modern humans. Although levels of distinction between the analyzed taxa (Homo, Pan, Gorilla, and Pongo) are generally corresponding to probable expectations based on their taxonomic rank, few exceptions were found. Notably, the craniodental morphology of Homo erectus showed a greater dissimilarity to other Homo species, where it consistently overlapped or grouped with Pan species on all ordination plots and clustering. In addition, the direct link between European humans and Neandertals, which is well-characterized on all of the phylogenetic trees based on maximum parsimony and maximum likelihood methods, was not outlined in the morphologic-based clustering. Both morphological and molecular distances between Neandertal and modern humans were consistently greater than the distances among modern humans, however, the distances are still smaller than those between any two distinct species (so they are subspecies). The topology of the phylogenetic trees based on the whole mtDNA has shown a minor discrepancy with the results obtained from the craniodental morphologies.}, }
@article {pmid31637998, year = {2019}, author = {Delgobo, M and Mendes, DA and Kozlova, E and Rocha, EL and Rodrigues-Luiz, GF and Mascarin, L and Dias, G and Patrício, DO and Dierckx, T and Bicca, MA and Bretton, G and Tenório de Menezes, YK and Starick, MR and Rovaris, D and Del Moral, J and Mansur, DS and Van Weyenbergh, J and Báfica, A}, title = {An evolutionary recent IFN/IL-6/CEBP axis is linked to monocyte expansion and tuberculosis severity in humans.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31637998}, issn = {2050-084X}, support = {G0D6817N//FWO/International ; Global Research Initiative Program TW008276/NH/NIH HHS/United States ; Early Career Scientist 55007412/HHMI/Howard Hughes Medical Institute/United States ; VLAIO IWT141614//Fonds Wetenschappelijk Onderzoek/International ; 23038.010048/2013-27//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/International ; PQ//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/International ; G0D6817N//Fonds Wetenschappelijk Onderzoek/International ; 23038.010048/2013-27//CAPES/International ; R01 TW008276/TW/FIC NIH HHS/United States ; }, mesh = {Antigens, CD34 ; CCAAT-Enhancer-Binding Proteins/genetics/*metabolism ; Cell Differentiation ; Cell Proliferation ; Cytokines/genetics/metabolism ; Genome-Wide Association Study ; Humans ; Hydrolases ; Interferons/genetics/*metabolism ; Interleukin-6/genetics/*metabolism ; Macrophages/microbiology ; Monocytes/*metabolism/microbiology ; Mycobacterium tuberculosis/*immunology/pathogenicity ; Myeloid Cells/physiology ; Proteomics ; Receptors, Interleukin-6 ; Severity of Illness Index ; Transcriptome ; Tuberculosis/*immunology/metabolism ; }, abstract = {Monocyte counts are increased during human tuberculosis (TB) but it has not been determined whether Mycobacterium tuberculosis (Mtb) directly regulates myeloid commitment. We demonstrated that exposure to Mtb directs primary human CD34[+] cells to differentiate into monocytes/macrophages. In vitro myeloid conversion did not require type I or type II IFN signaling. In contrast, Mtb enhanced IL-6 responses by CD34[+] cell cultures and IL-6R neutralization inhibited myeloid differentiation and decreased mycobacterial growth in vitro. Integrated systems biology analysis of transcriptomic, proteomic and genomic data of large data sets of healthy controls and TB patients established the existence of a myeloid IL-6/IL6R/CEBP gene module associated with disease severity. Furthermore, genetic and functional analysis revealed the IL6/IL6R/CEBP gene module has undergone recent evolutionary selection, including Neanderthal introgression and human pathogen adaptation, connected to systemic monocyte counts. These results suggest Mtb co-opts an evolutionary recent IFN-IL6-CEBP feed-forward loop, increasing myeloid differentiation linked to severe TB in humans.}, }
@article {pmid31636221, year = {2019}, author = {Zilhão, J}, title = {Tar adhesives, Neandertals, and the tyranny of the discontinuous mind.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {44}, pages = {21966-21968}, pmid = {31636221}, issn = {1091-6490}, mesh = {Adhesives ; Fossils ; Humans ; *Neanderthals ; North Sea ; Technology ; }, }
@article {pmid31636186, year = {2019}, author = {Niekus, MJLT and Kozowyk, PRB and Langejans, GHJ and Ngan-Tillard, D and van Keulen, H and van der Plicht, J and Cohen, KM and van Wingerden, W and van Os, B and Smit, BI and Amkreutz, LWSW and Johansen, L and Verbaas, A and Dusseldorp, GL}, title = {Middle Paleolithic complex technology and a Neandertal tar-backed tool from the Dutch North Sea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {44}, pages = {22081-22087}, pmid = {31636186}, issn = {1091-6490}, mesh = {Adhesives ; Animals ; *Archaeology ; Humans ; Neanderthals ; Netherlands ; Technology ; *Tool Use Behavior ; X-Ray Microtomography ; }, abstract = {We report the discovery of a 50,000-y-old birch tar-hafted flint tool found off the present-day coastline of The Netherlands. The production of adhesives and multicomponent tools is considered complex technology and has a prominent place in discussions about the evolution of human behavior. This find provides evidence on the technological capabilities of Neandertals and illuminates the currently debated conditions under which these technologies could be maintained. [14]C-accelerator mass spectrometry dating and the geological provenance of the artifact firmly associates it with a host of Middle Paleolithic stone tools and a Neandertal fossil. The find was analyzed using pyrolysis-gas chromatography-mass spectrometry, X-ray micro-computed tomography, and optical light microscopy. The object is a piece of birch tar, encompassing one-third of a flint flake. This find is from northwestern Europe and complements a small set of well-dated and chemically identified adhesives from Middle Paleolithic/Middle Stone Age contexts. Together with data from experiments and other Middle Paleolithic adhesives, it demonstrates that Neandertals mastered complex adhesive production strategies and composite tool use at the northern edge of their range. Thus, a large population size is not a necessary condition for complex behavior and technology. The mitigation of ecological risk, as demonstrated by the challenging conditions during Marine Isotope Stage 4 and 3, provides a better explanation for the transmission and maintenance of technological complexity.}, }
@article {pmid31629539, year = {2021}, author = {Borgel, S and Latimer, B and McDermott, Y and Sarig, R and Pokhojaev, A and Abulafia, T and Goder-Goldberger, M and Barzilai, O and May, H}, title = {Early Upper Paleolithic human foot bones from Manot Cave, Israel.}, journal = {Journal of human evolution}, volume = {160}, number = {}, pages = {102668}, doi = {10.1016/j.jhevol.2019.102668}, pmid = {31629539}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Caves ; Foot Bones ; Fossils ; Humans ; Israel ; *Neanderthals ; }, abstract = {The transition from the Middle Paleolithic to the Upper Paleolithic in the Levant represents a major event in human prehistory with regards to the dispersal of modern human populations. Unfortunately, the scarcity of human remains from this period has hampered our ability to study the anatomy of Upper Paleolithic populations. This study describes and examines pedal bones recovered from the Early Upper Paleolithic period at Manot Cave, Israel, from 2014 to 2017. The Manot Cave foot bones include a partial, left foot skeleton comprising a talus, a calcaneus, a cuboid, a first metatarsal, a second metatarsal, a fifth metatarsal, and a hallucal sesamoid. All these remains were found in the same archaeological unit of the cave and belong to a young adult. Shape and size comparisons with Neanderthals, Anatomically Modern Human and modern human foot bones indicate a modern human morphology. In some characteristics, however, the Manot Cave foot bones display a Neanderthal-like pattern. Notably, the Manot Cave foot is remarkable in its overall gracility. A healed traumatic injury in the second metatarsal (Lisfranc's fracture) is most likely due to a remote impact to the dorsum of the foot. This injury, its subsequent debility, and the individual's apparent recovery suggest that the members of the Manot Cave community had a supportive environment, one with mutual responsibilities among the members.}, }
@article {pmid31624180, year = {2019}, author = {Hsieh, P and Vollger, MR and Dang, V and Porubsky, D and Baker, C and Cantsilieris, S and Hoekzema, K and Lewis, AP and Munson, KM and Sorensen, M and Kronenberg, ZN and Murali, S and Nelson, BJ and Chiatante, G and Maggiolini, FAM and Blanché, H and Underwood, JG and Antonacci, F and Deleuze, JF and Eichler, EE}, title = {Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6463}, pages = {}, pmid = {31624180}, issn = {1095-9203}, support = {/HHMI_/Howard Hughes Medical Institute/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Chromosome Duplication ; Chromosomes, Human, Pair 16/genetics ; Chromosomes, Human, Pair 8/genetics ; DNA Copy Number Variations ; Evolution, Molecular ; *Genetic Introgression ; Genome, Human ; Haplotypes ; Hominidae/genetics ; Humans ; Melanesia ; Models, Genetic ; Neanderthals/genetics ; Polymorphism, Genetic ; Selection, Genetic ; Whole Genome Sequencing ; }, abstract = {Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation.}, }
@article {pmid31621987, year = {2019}, author = {Tryon, CA}, title = {The Middle/Later Stone Age transition and cultural dynamics of late Pleistocene East Africa.}, journal = {Evolutionary anthropology}, volume = {28}, number = {5}, pages = {267-282}, doi = {10.1002/evan.21802}, pmid = {31621987}, issn = {1520-6505}, mesh = {Africa, Eastern ; Animals ; *Archaeology ; *Biological Evolution ; *Cultural Evolution ; History, Ancient ; Humans ; Neanderthals ; Technology/history ; Tool Use Behavior ; }, abstract = {The Middle to Later Stone Age (MSA/LSA) transition is a prominent feature of the African archeological record that began in some places ~30,000-60,000 years ago, historically associated with the origin and/or dispersal of "modern" humans. Unlike the analogous Middle to Upper Paleolithic transition in Eurasia and associated Neanderthal extinction, the African MSA/LSA record remains poorly documented, with its potential role in explaining changes in the behavioral diversity and geographic range of Homo sapiens largely unexplored. I review archeological and biogeographic data from East Africa, show regionally diverse pathways to the MSA/LSA transition, and emphasize the need for analytical approaches that document potential ancestor-descendent relationships visible in the archeological record, needed to assess independent invention, population interaction, dispersal, and other potential mechanisms for behavioral change. Diversity within East Africa underscores the need for regional, rather than continental-scale narratives of the later evolutionary history of H. sapiens.}, }
@article {pmid31614276, year = {2019}, author = {Pan, L and Dumoncel, J and Mazurier, A and Zanolli, C}, title = {Structural analysis of premolar roots in Middle Pleistocene hominins from China.}, journal = {Journal of human evolution}, volume = {136}, number = {}, pages = {102669}, doi = {10.1016/j.jhevol.2019.102669}, pmid = {31614276}, issn = {1095-8606}, mesh = {Animals ; Bicuspid/*anatomy &amp; histology ; *Biological Evolution ; China ; Fossils/*anatomy &amp; histology ; Hominidae/*anatomy &amp; histology ; Mandible ; Maxilla ; Tooth Root/*anatomy &amp; histology ; }, abstract = {This study investigates permanent maxillary and mandibular premolar root structural organization in East Asian Middle Pleistocene hominins. In addition to reporting and analyzing the linear and volumetric properties of the roots, we used a landmark-free approach to both qualify and quantify in 3D premolar root shape variation of Middle Pleistocene hominins in East Asia. Moreover, we focus on some mid-to late East Asian Middle Pleistocene hominin specimens whose taxonomic attribution is unclear. We find considerable cementum in this sample of hominins, similar to other fossil groups, but clearly different from modern humans which have a very small amount of cementum. Additionally, a smaller root pulp cavity is found in later Homo (Neanderthals and modern humans). Our analyses on the crown-root surface area ratio show that East Asian Middle Pleistocene Homo erectus as well as one late Middle Pleistocene Homo sp. specimen (PA 81 P4 from Changyang site) are distinguished from other fossil and extant groups by a relatively larger root surface, stout root branches and thick cementum deposits. This may represent a distinct East Asian H. erectus dental pattern. Geometric morphometric analyses on the external root surface reveal a general trend of shape simplification along the Homo lineage examined here, and distinguish Early Pleistocene Homo, Middle Pleistocene H. erectus, Neanderthals and modern human morphologies. The late Middle Pleistocene teeth from Changyang site (PA 76 P[3] and PA 81 P[4]) are close to East Asian H. erectus and Neanderthals, while the mid-Middle Pleistocene P3 from Panxian Dadong falls within the modern human distribution. Combined with dental crown morphology and root number/form reported in previous studies, our results show that the external root shape can be considered a taxonomically relevant indicator. In general, an evolutionary tendency towards modern human morphology is observed in part of the East Asian Middle Pleistocene specimens, while a retention of primitive, H. erectus-like features is expressed in some late Middle Pleistocene specimens, supporting a multi-lineage and discontinuous scenario of human settlements in East Asia.}, }
@article {pmid31611012, year = {2021}, author = {Sarig, R and Fornai, C and Pokhojaev, A and May, H and Hans, M and Latimer, B and Barzilai, O and Quam, R and Weber, GW}, title = {The dental remains from the Early Upper Paleolithic of Manot Cave, Israel.}, journal = {Journal of human evolution}, volume = {160}, number = {}, pages = {102648}, doi = {10.1016/j.jhevol.2019.102648}, pmid = {31611012}, issn = {1095-8606}, support = {176319/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Animals ; Caves ; *Fossils ; Humans ; Israel ; *Neanderthals ; Tooth, Deciduous ; }, abstract = {This study presents the dental remains discovered at Manot Cave (MC), Western Galilee, Israel. The cave contains evidence for human occupation during the Early Upper Paleolithic period (46-33 ka) mainly of Early Ahmarian (∼46-42 ka) and Levantine Aurignacian (∼38-34 ka) cultural levels. Six teeth (three deciduous and three permanent) were found at the site, of which four could be thoroughly analyzed. The morphology of the teeth was qualitatively described and analyzed using traditional and geometric morphometric methods. A large comparative sample was used in order to assess the morphological affiliation of the Manot specimens with other Homo groups. The results provided equivocal signals: the upper first premolar (MC-9 P[3]) is probably modern human; the upper deciduous second molar (MC-10 dm[2]) and the upper second permanent molar (MC-8 M[2]) might be modern humans; the lower second deciduous molar (MC-7 dm2) might be Neanderthal. Owing to the small sample size and the almost total lack of distinctive characteristics, our outcome could not supply conclusive evidence to address the question of whether Manot Aurignacian population came from Europe or descended from the local Ahmarian population.}, }
@article {pmid31604218, year = {2019}, author = {Price, M}, title = {Face of the mysterious Denisovans emerges.}, journal = {Science (New York, N.Y.)}, volume = {365}, number = {6459}, pages = {1232}, doi = {10.1126/science.365.6459.1232}, pmid = {31604218}, issn = {1095-9203}, mesh = {Animals ; Asia ; *Biological Evolution ; DNA Methylation ; Epigenesis, Genetic ; Extinction, Biological ; Hominidae/*classification ; Neanderthals ; }, }
@article {pmid31591491, year = {2019}, author = {Colbran, LL and Gamazon, ER and Zhou, D and Evans, P and Cox, NJ and Capra, JA}, title = {Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {11}, pages = {1598-1606}, pmid = {31591491}, issn = {2397-334X}, support = {R01 MH113362/MH/NIMH NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; R35 HG010718/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Female ; Genome, Human ; Haplotypes ; *Hominidae ; Humans ; *Neanderthals ; Phenotype ; }, abstract = {Sequencing DNA derived from archaic bones has enabled genetic comparison of Neanderthals and anatomically modern humans (AMHs), and revealed that they interbred. However, interpreting what genetic differences imply about their phenotypic differences remains challenging. Here, we introduce an approach for identifying divergent gene regulation between archaic hominins, such as Neanderthals, and AMH sequences, and find 766 genes that are likely to have been divergently regulated (DR) by Neanderthal haplotypes that do not remain in AMHs. DR genes include many involved in phenotypes known to differ between Neanderthals and AMHs, such as the structure of the rib cage and supraorbital ridge development. They are also enriched for genes associated with spontaneous abortion, polycystic ovary syndrome, myocardial infarction and melanoma. Phenotypes associated with modern human variation in these genes' regulation in ~23,000 biobank patients further support their involvement in immune and cardiovascular phenotypes. Comparing DR genes between two Neanderthals and a Denisovan revealed divergence in the immune system and in genes associated with skeletal and dental morphology that are consistent with the archaeological record. These results establish differences in gene regulatory architecture between AMHs and archaic hominins, and provide an avenue for exploring phenotypic differences between archaic groups from genomic information alone.}, }
@article {pmid31589589, year = {2019}, author = {Eisová, S and Velemínský, P and Bruner, E}, title = {The Neanderthal endocast from Gánovce (Poprad, Slovak Republic).}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {96}, number = {}, pages = {139-149}, doi = {10.4436/JASS.97005}, pmid = {31589589}, issn = {2037-0644}, mesh = {Animals ; Brain/anatomy &amp; histology ; Hominidae/anatomy &amp; histology ; Humans ; Neanderthals/*anatomy &amp; histology/classification/physiology ; Paleontology ; Skull/*anatomy &amp; histology ; Slovakia ; }, abstract = {A Neanderthal endocast, naturally formed by travertine within the crater of a thermal spring, was found at Gánovce, near Poprad (Slovakia), in 1926, and dated to 105 ka. The endocast is partially covered by fragments of the braincase. The volume of the endocast was estimated to be 1320 cc. The endocast was first studied by the Czech paleoanthropologist Emanuel Vlček, who performed metric and morphological analyses which suggested its Neanderthal origin. Vlček published his works more than fifty years ago, but the fossil is scarcely known to the general paleoanthropological community, probably because of language barriers. Here, we review the historical and anatomical information available on the endocasts, providing additional paleoneurological assessments on its features. The endocast displays typical Neanderthal traits, and its overall appearance is similar to Guattari 1, mostly because of the pronounced frontal width and occipital bulging. The morphology of the Gánovce specimen suggests once more that the Neanderthal endocranial phenotype had already evolved at 100 ka.}, }
@article {pmid31586143, year = {2019}, author = {Sánchez-Hernández, C and Gourichon, L and Pubert, E and Rendu, W and Montes, R and Rivals, F}, title = {Combined dental wear and cementum analyses in ungulates reveal the seasonality of Neanderthal occupations in Covalejos Cave (Northern Iberia).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14335}, pmid = {31586143}, issn = {2045-2322}, mesh = {Animals ; *Biological Evolution ; Caves ; Dental Cementum/*chemistry/physiopathology ; Feeding Behavior/*physiology ; Fossils ; Neanderthals/*physiology ; Population Dynamics ; Seasons ; Tooth Wear/*physiopathology ; }, abstract = {We propose for the first time the use of the combination of two high-resolution techniques, dental wear (meso- and microwear) and dental cementum analyses, to gain a better understanding of Neanderthal subsistence strategies and occupational patterns. Dental wear analysis provides information not only on ungulate palaeodiet and palaeoenvironments but also on hunting time and seasons. Dental cementum analysis allows the accurate determination of the age and season at death of a prey. Our study has focused on the Cantabrian region and has applied both methods to investigate the Mousterian faunal assemblages in Covalejos Cave. Identification of the ungulate palaeodiet reveals information on the environmental conditions of the studied region. Moreover, it may facilitate observation on the evolution of both palaeodiet and palaeoenvironment throughout the site sequence. Results show a general stability in the palaeoenvironmental conditions and in the ungulate palaeodiet throughout the Mousterian sequence; this finding may be attributed to the role of the area as a climate refuge, and slight differences in levels 8, 7 and 4 suggest long- or short-term but repeated Neanderthal occupations at different seasons in the annual cycle.}, }
@article {pmid31585375, year = {2019}, author = {Davies, TW and Delezene, LK and Gunz, P and Hublin, JJ and Skinner, MM}, title = {Endostructural morphology in hominoid mandibular third premolars: Discrete traits at the enamel-dentine junction.}, journal = {Journal of human evolution}, volume = {136}, number = {}, pages = {102670}, doi = {10.1016/j.jhevol.2019.102670}, pmid = {31585375}, issn = {1095-8606}, mesh = {Animals ; Bicuspid/*anatomy &amp; histology/growth &amp; development ; Dental Enamel/anatomy &amp; histology ; Dentin/anatomy &amp; histology ; Hominidae/*anatomy &amp; histology/growth &amp; development ; Mandible ; }, abstract = {The mandibular third premolar (P3) exhibits substantial differences in size and shape among hominoid taxa, and displays a number of discrete traits that have proven to be useful in studies of hominin taxonomy and phylogeny. Discrete traits at the enamel-dentine junction (EDJ) can be accurately assessed on moderately worn specimens, and often appear sharper than at the outer-enamel surface (OES). Here we use microtomography to image the P3 EDJ of a broad sample of extant apes, extinct hominins and modern humans (n = 100). We present typologies for three important premolar discrete traits at the EDJ (transverse crest, marginal ridge and buccal grooves), and score trait frequencies within our sample. We find that the transverse crest is variable in extant apes, while the majority of hominins display a transverse crest which runs directly between the two major premolar cusps. Some Neanderthals display a unique form in which the transverse crest fails to reach the protoconid. We find that mesial marginal ridge discontinuity is common in Australopithecus anamensis and Australopithecus afarensis while continuous marginal ridges largely characterize Australopithecus africanus and Paranthropus. Interrupted mesial and distal marginal ridges are again seen in Homo sapiens and Neanderthals. Premolar buccal grooves, previously identified at the OES as important for hominin systematics, are again found to show a number of taxon-specific patterns at the EDJ, including a clear difference between Australopithecus and Paranthropus specimens. However, their appearance may be dependent on the morphology of other parts of the crown such as the protoconid crest, and the presence of accessory dentine horns. Finally, we discuss rare variations in the form of dentine horns that underlie premolar cusps, and their potential homology to similar morphologies in other tooth positions.}, }
@article {pmid31569005, year = {2019}, author = {Conde-Valverde, M and Martínez, I and Quam, RM and Bonmatí, A and Lorenzo, C and Velez, AD and Martínez-Calvo, C and Arsuaga, JL}, title = {The cochlea of the Sima de los Huesos hominins (Sierra de Atapuerca, Spain): New insights into cochlear evolution in the genus Homo.}, journal = {Journal of human evolution}, volume = {136}, number = {}, pages = {102641}, doi = {10.1016/j.jhevol.2019.102641}, pmid = {31569005}, issn = {1095-8606}, mesh = {Animals ; *Biological Evolution ; Cochlea/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Hominidae/anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Spain ; }, abstract = {The cochlea contains taxonomic and phylogenetic information and its morphology is related with hearing abilities among fossil hominins. Data for the genus Homo is presently limited to early Homo and the early Neandertals from Krapina. The present study of the middle Pleistocene hominins from the Sima de los Huesos (SH) provides new evidence on cochlear evolution in the genus Homo. We compared the absolute length, proportional lengths of each turn, number of turns, size and shape of the cross-section of the basal turn, volume, curvature gradient, and thickness of the cochlea between extant Pan troglodytes, extant Homo sapiens, Homo neanderthalensis and the SH hominins. The SH hominins resemble P. troglodytes in the proportionally long basal turn, the small size and round shape of the cross-section of the basal turn, the small cochlear volume and the low cochlear thickness. The SH hominins resemble Neandertals and H. sapiens in their long cochlear length and in the proportionally short third turn. Homo neanderthalensis and H. sapiens share several features, not present in the SH hominins, and that likely represent homoplasies: a larger volume, larger size and oval shape of the cross-section of the basal turn and higher cochlear thickness. Later Neandertals show a derived proportionally shorter apical turn. Changes in cochlear volume in Homo cannot be fully explained by variation in body mass or cochlear length but are more directly related to changes in the cross-sectional area of the basal turn. Based on previous studies of the outer and middle ear in SH hominins, changes in the outer and middle ear preceded changes in the inner ear, and the cochlea and semicircular canals seem to have evolved independently in the Neandertal clade. Finally, the small cochlear volume in the SH hominins suggests a slightly higher upper limit of hearing compared with modern humans.}, }
@article {pmid31560950, year = {2019}, author = {Mata, X and Renaud, G and Mollereau, C}, title = {The repertoire of family A-peptide GPCRs in archaic hominins.}, journal = {Peptides}, volume = {122}, number = {}, pages = {170154}, doi = {10.1016/j.peptides.2019.170154}, pmid = {31560950}, issn = {1873-5169}, mesh = {Animals ; Diabetic Nephropathies/*genetics/pathology ; *Evolution, Molecular ; Genome, Human/genetics ; Haplotypes/genetics ; Hominidae/genetics ; Humans ; Neanderthals/genetics ; Obesity/*genetics/pathology ; Peptides/genetics ; Platelet Aggregation/genetics ; Receptors, G-Protein-Coupled/*genetics ; Risk Factors ; }, abstract = {Given the importance of G-protein coupled receptors in the regulation of many physiological functions, deciphering the relationships between genotype and phenotype in past and present hominin GPCRs is of main interest to understand the evolutionary process that contributed to the present-day variability in human traits and health. Here, we carefully examined the publicly available genomic and protein sequence databases of the archaic hominins (Neanderthal and Denisova) to draw up the catalog of coding variations in GPCRs for peptide ligands, in comparison with living humans. We then searched in the literature the functional changes, phenotypes and risk of disease possibly associated with the detected variants. Our survey suggests that Neanderthal and Denisovan hominins were likely prone to lower risk of obesity, to enhanced platelet aggregation in response to thrombin, to better response to infection, to less anxiety and aggressiveness and to favorable sociability. While some archaic variants were likely advantageous in the past, they might be responsible for maladaptive disorders today in the context of modern life and/or specific regional distribution. For example, an archaic haplotype in the neuromedin receptor 2 is susceptible to confer risk of diabetic nephropathy in type 1 diabetes in present-day Europeans. Paying attention to the pharmacological properties of some of the archaic variants described in this study may be helpful to understand the variability of therapeutic efficacy between individuals or ethnic groups.}, }
@article {pmid31558829, year = {2019}, author = {Sano, K and Arrighi, S and Stani, C and Aureli, D and Boschin, F and Fiore, I and Spagnolo, V and Ricci, S and Crezzini, J and Boscato, P and Gala, M and Tagliacozzo, A and Birarda, G and Vaccari, L and Ronchitelli, A and Moroni, A and Benazzi, S}, title = {The earliest evidence for mechanically delivered projectile weapons in Europe.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {10}, pages = {1409-1414}, pmid = {31558829}, issn = {2397-334X}, support = {724046/ERC_/European Research Council/International ; }, mesh = {Europe ; Fossils ; Humans ; Italy ; *Neanderthals ; Weapons ; }, abstract = {Microscopic analysis of backed lithic pieces from the Uluzzian technocomplex (45-40 thousand yr ago) at Grotta del Cavallo (southern Italy) reveals their use as mechanically delivered projectile weapons, attributed to anatomically modern humans. Use-wear and residue analyses indicate that the lithics were hunting armatures hafted with complex adhesives, while experimental and ethnographic comparisons support their use as projectiles. The use of projectiles conferred a hunting strategy with a higher impact energy and a potential subsistence advantage over other populations and species.}, }
@article {pmid31558742, year = {2019}, author = {Morley, MW and Goldberg, P and Uliyanov, VA and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Jacobs, Z and Roberts, RG}, title = {Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13785}, pmid = {31558742}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; *Caves ; Cold Climate ; DNA, Ancient/isolation &amp; purification ; *Fossils ; History, Ancient ; *Hominidae/genetics ; Humans ; Neanderthals/genetics ; Paleontology ; Siberia ; }, abstract = {Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal-Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.}, }
@article {pmid31551725, year = {2019}, author = {Benítez-Burraco, A and Murphy, E}, title = {Why Brain Oscillations Are Improving Our Understanding of Language.}, journal = {Frontiers in behavioral neuroscience}, volume = {13}, number = {}, pages = {190}, pmid = {31551725}, issn = {1662-5153}, abstract = {We explore the potential that brain oscillations have for improving our understanding of how language develops, is processed in the brain, and initially evolved in our species. The different synchronization patterns of brain rhythms can account for different perceptual and cognitive functions, and we argue that this includes language. We aim to address six distinct questions-the What, How, Where, Who, Why, and When questions-pertaining to oscillatory investigations of language. Language deficits found in clinical conditions like autism, schizophrenia and dyslexia can be satisfactorily construed in terms of an abnormal, disorder-specific pattern of brain rhythmicity. Lastly, an eco-evo-devo approach to language is defended with explicit reference to brain oscillations, embracing a framework that considers language evolution to be the result of a changing environment surrounding developmental paths of the primate brain.}, }
@article {pmid31551547, year = {2019}, author = {Callaway, E}, title = {First portrait of mysterious Denisovans drawn from DNA.}, journal = {Nature}, volume = {573}, number = {7775}, pages = {475-476}, pmid = {31551547}, issn = {1476-4687}, mesh = {Animals ; DNA ; DNA Methylation ; Fossils ; Hominidae/*genetics ; Neanderthals/*genetics ; }, }
@article {pmid31546194, year = {2019}, author = {Bailey, SE and Brophy, JK and Moggi-Cecchi, J and Delezene, LK}, title = {The deciduous dentition of Homo naledi: A comparative study.}, journal = {Journal of human evolution}, volume = {136}, number = {}, pages = {102655}, doi = {10.1016/j.jhevol.2019.102655}, pmid = {31546194}, issn = {1095-8606}, mesh = {Animals ; Fossils/*anatomy &amp; histology ; Hominidae/*anatomy &amp; histology/growth &amp; development ; Humans ; Neanderthals/anatomy &amp; histology/growth &amp; development ; Tooth, Deciduous/*anatomy &amp; histology/growth &amp; development ; }, abstract = {In 2013, 2014 new hominin remains were uncovered in the Dinaledi chamber of the Rising Star cave system in South Africa. In 2015 Berger and colleagues identified these remains as belonging to a new species Homo naledi (Berger et al., 2015). Subsequent comparative studies of the skull, postcrania and permanent dentition have supported this taxonomic affiliation (Harcourt-Smith et al., 2015; Kivell et al., 2015; Irish et al., 2018). The deciduous teeth can offer unique insights into hominin evolution. Due to their early onset and rapid development their morphology is thought to be under stronger genetic control and less influenced by environment than are the permanent teeth. In this study we compared the H. naledi deciduous teeth from the 2013-2014 excavations to samples representing much of the hominin clade including Australopithecus afarensis, Australopithecus africanus, Paranthropus boisei, Paranthropus robustus, early Homo, Homo antecessor, Homo erectus s.l., Homo floresiensis, Middle Pleistocene Homo, Homo neanderthalensis, early Homo sapiens and recent H. sapiens from Sub-Saharan Africa. By making such a broad morphological comparison, we aimed to contextualize the Dinaledi hominins and to further assess the validity of their taxonomic assignment. Our analysis of the deciduous teeth revealed a unique combination of features that mirror (but also expand) that found in the permanent teeth. This mosaic includes an asymmetrical lower canine with a distal tubercle, an upper first molar with a large hypocone and epicrista associated with a mesial cuspule, a molarized lower first molar resembling Paranthropus, and upper and lower second molars that resemble later Homo in their lack of accessory cusps. The unique combination of deciduous dental characters supports previous studies assigning H. naledi to a new species, although its phylogenetic position vis-à-vis other Homo species remains ambiguous.}, }
@article {pmid31539495, year = {2019}, author = {Gokhman, D and Mishol, N and de Manuel, M and de Juan, D and Shuqrun, J and Meshorer, E and Marques-Bonet, T and Rak, Y and Carmel, L}, title = {Reconstructing Denisovan Anatomy Using DNA Methylation Maps.}, journal = {Cell}, volume = {179}, number = {1}, pages = {180-192.e10}, doi = {10.1016/j.cell.2019.08.035}, pmid = {31539495}, issn = {1097-4172}, mesh = {Animals ; Base Sequence ; DNA Methylation/*genetics ; Databases, Genetic ; Extinction, Biological ; Fossils ; Genome, Human/genetics ; Humans ; Neanderthals/*anatomy &amp; histology/*genetics ; Pan troglodytes/*anatomy &amp; histology/*genetics ; *Phenotype ; Polymorphism, Single Nucleotide/genetics ; Skeleton ; Skull ; }, abstract = {Denisovans are an extinct group of humans whose morphology remains unknown. Here, we present a method for reconstructing skeletal morphology using DNA methylation patterns. Our method is based on linking unidirectional methylation changes to loss-of-function phenotypes. We tested performance by reconstructing Neanderthal and chimpanzee skeletal morphologies and obtained >85% precision in identifying divergent traits. We then applied this method to the Denisovan and offer a putative morphological profile. We suggest that Denisovans likely shared with Neanderthals traits such as an elongated face and a wide pelvis. We also identify Denisovan-derived changes, such as an increased dental arch and lateral cranial expansion. Our predictions match the only morphologically informative Denisovan bone to date, as well as the Xuchang skull, which was suggested by some to be a Denisovan. We conclude that DNA methylation can be used to reconstruct anatomical features, including some that do not survive in the fossil record.}, }
@article {pmid31538229, year = {2019}, author = {Hanke, B}, title = {[On the relationship between Neanderthal alleles and cytotoxicity].}, journal = {Der Pathologe}, volume = {40}, number = {6}, pages = {627-628}, pmid = {31538229}, issn = {1432-1963}, mesh = {*Alleles ; Animals ; Humans ; *Neanderthals/genetics ; }, }
@article {pmid31521027, year = {2019}, author = {Conde-Valverde, M and Rosa, M and Martínez, I and Marchamalo, J and Pantoja-Pérez, A and Quam, R and Lorenzo, C and Gracia-Téllez, A and García-Fernández, A and Arsuaga, JL and Rivera-Rodríguez, T}, title = {A revision of the conductive hearing loss in Cranium 4 from the Middle Pleistocene site of Sima de los Huesos (Burgos, Spain).}, journal = {Journal of human evolution}, volume = {135}, number = {}, pages = {102663}, doi = {10.1016/j.jhevol.2019.102663}, pmid = {31521027}, issn = {1095-8606}, mesh = {Animals ; Hearing Loss/*pathology ; Hominidae ; Male ; *Neanderthals ; Spain ; }, abstract = {Pathological conditions have been previously documented in the Middle Pleistocene Sima de los Huesos hominins from northern Spain, and several of these have clear behavioral implications. Within this fossil assemblage, Cranium 4 shows bilateral external auditory exostoses which have been preliminarily interpreted as causing a significant hearing loss in this individual. If confirmed, this would be the oldest recorded case of deafness in human history and could have important implications for the antiquity of this condition, as well as social interactions. To further investigate this case, the current study presents 3D reconstructions of the entire outer and middle ear, based on computed tomography scans of both temporal bones in Cranium 4. We established the degree of stenosis in both external auditory canals, showing that in both cases the degree of stenosis is less than 52% of the original cross-sectional area of each canal. Based on clinical studies in living humans, the buildup of wax due to the degree of stenosis in Cranium 4 is unlikely to have caused frequent external ear infections. In addition, we estimated the pattern of sound power transmission up to 5 kHz in both ears relying on a comprehensive model developed in the bioengineering literature and which has been applied previously to the Sima de los Huesos hominins. The model was modified to account for the peculiar shape of the pathological external ear canals in Cranium 4. The results show that this pathology had little to no influence on the sound power transmission in this individual. Thus, we conclude that the exostoses present in both ears of Cranium 4 did not significantly affect their hearing.}, }
@article {pmid31517046, year = {2019}, author = {Bennett, EA and Crevecoeur, I and Viola, B and Derevianko, AP and Shunkov, MV and Grange, T and Maureille, B and Geigl, EM}, title = {Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals.}, journal = {Science advances}, volume = {5}, number = {9}, pages = {eaaw3950}, pmid = {31517046}, issn = {2375-2548}, mesh = {Animals ; Finger Phalanges/*anatomy &amp; histology ; *Genome, Human ; Humans ; Molar/*anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology/genetics ; Species Specificity ; }, abstract = {A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans.}, }
@article {pmid31517044, year = {2019}, author = {Raveane, A and Aneli, S and Montinaro, F and Athanasiadis, G and Barlera, S and Birolo, G and Boncoraglio, G and Di Blasio, AM and Di Gaetano, C and Pagani, L and Parolo, S and Paschou, P and Piazza, A and Stamatoyannopoulos, G and Angius, A and Brucato, N and Cucca, F and Hellenthal, G and Mulas, A and Peyret-Guzzon, M and Zoledziewska, M and Baali, A and Bycroft, C and Cherkaoui, M and Chiaroni, J and Di Cristofaro, J and Dina, C and Dugoujon, JM and Galan, P and Giemza, J and Kivisild, T and Mazieres, S and Melhaoui, M and Metspalu, M and Myers, S and Pereira, L and Ricaut, FX and Brisighelli, F and Cardinali, I and Grugni, V and Lancioni, H and Pascali, VL and Torroni, A and Semino, O and Matullo, G and Achilli, A and Olivieri, A and Capelli, C}, title = {Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe.}, journal = {Science advances}, volume = {5}, number = {9}, pages = {eaaw3492}, pmid = {31517044}, issn = {2375-2548}, mesh = {Animals ; *DNA, Ancient ; *Databases, Genetic ; *Genetic Drift ; *Genome, Human ; Genome-Wide Association Study ; History, Ancient ; Human Genetics ; Humans ; Italy ; Neanderthals/genetics ; Whites/*genetics ; }, abstract = {European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.}, }
@article {pmid31506618, year = {2019}, author = {Callaway, E}, title = {Lost Denisovan bone reveals surprisingly human-like finger.}, journal = {Nature}, volume = {573}, number = {7773}, pages = {175-176}, pmid = {31506618}, issn = {1476-4687}, mesh = {Animals ; Archaeology ; Fingers ; *Hominidae ; Humans ; *Neanderthals ; }, }
@article {pmid31506422, year = {2019}, author = {Mounier, A and Mirazón Lahr, M}, title = {Deciphering African late middle Pleistocene hominin diversity and the origin of our species.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3406}, pmid = {31506422}, issn = {2041-1723}, mesh = {Africa ; Animals ; *Biodiversity ; Fossils/anatomy &amp; histology ; Hominidae/anatomy &amp; histology/*physiology ; Humans ; *Models, Biological ; *Phylogeny ; Phylogeography ; Skull/anatomy &amp; histology ; }, abstract = {The origin of Homo sapiens remains a matter of debate. The extent and geographic patterning of morphological diversity among Late Middle Pleistocene (LMP) African hominins is largely unknown, thus precluding the definition of boundaries of variability in early H. sapiens and the interpretation of individual fossils. Here we use a phylogenetic modelling method to predict possible morphologies of a last common ancestor of all modern humans, which we compare to LMP African fossils (KNM-ES 11693, Florisbad, Irhoud 1, Omo II, and LH18). Our results support a complex process for the evolution of H. sapiens, with the recognition of different, geographically localised, populations and lineages in Africa - not all of which contributed to our species' origin. Based on the available fossils, H. sapiens appears to have originated from the coalescence of South and, possibly, East-African source populations, while North-African fossils may represent a population which introgressed into Neandertals during the LMP.}, }
@article {pmid31501334, year = {2019}, author = {Duveau, J and Berillon, G and Verna, C and Laisné, G and Cliquet, D}, title = {The composition of a Neandertal social group revealed by the hominin footprints at Le Rozel (Normandy, France).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {39}, pages = {19409-19414}, pmid = {31501334}, issn = {1091-6490}, mesh = {Animals ; Archaeology ; Foot/*anatomy &amp; histology ; *Fossils ; France ; Neanderthals/*anatomy &amp; histology ; Sociological Factors ; }, abstract = {Footprints represent a unique snapshot of hominin life. They provide information on the size and composition of groups that differs from osteological and archeological remains, whose contemporaneity is difficult to establish. We report here on the discovery of 257 footprints dated to 80,000 y from the Paleolithic site at Le Rozel (Normandy, France), which represent the largest known Neandertal ichnological assemblage to date. We investigate the size and composition of a track-maker group from this large set by developing a morphometric method based on experimental footprints. Our analyses indicate that the footprints were made by a small group comprising different age classes, from early childhood to adult, with a majority of children. The Le Rozel footprints thus provide direct evidence for the size and composition of a Neandertal social group.}, }
@article {pmid31477933, year = {2019}, author = {Speidel, L and Forest, M and Shi, S and Myers, SR}, title = {A method for genome-wide genealogy estimation for thousands of samples.}, journal = {Nature genetics}, volume = {51}, number = {9}, pages = {1321-1329}, pmid = {31477933}, issn = {1546-1718}, support = {098387/Z/12/Z//Wellcome Trust (Wellcome)/International ; 098387/WT_/Wellcome Trust/United Kingdom ; 203141/WT_/Wellcome Trust/United Kingdom ; 212284/WT_/Wellcome Trust/United Kingdom ; 220457/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 203141/Z/16/Z//Wellcome Trust (Wellcome)/International ; 212284/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 212284/Z/18/Z//Wellcome Trust (Wellcome)/International ; }, mesh = {Animals ; *Evolution, Molecular ; *Genetics, Population ; *Genome, Human ; Genome-Wide Association Study/*methods ; Haplotypes ; Humans ; Mutation ; Neanderthals ; *Pedigree ; Polymorphism, Single Nucleotide ; Population Density ; *Selection, Genetic ; }, abstract = {Knowledge of genome-wide genealogies for thousands of individuals would simplify most evolutionary analyses for humans and other species, but has remained computationally infeasible. We have developed a method, Relate, scaling to >10,000 sequences while simultaneously estimating branch lengths, mutational ages and variable historical population sizes, as well as allowing for data errors. Application to 1,000 Genomes Project haplotypes produces joint genealogical histories for 26 human populations. Highly diverged lineages are present in all groups, but most frequent in Africa. Outside Africa, these mainly reflect ancient introgression from groups related to Neanderthals and Denisovans, while African signals instead reflect unknown events unique to that continent. Our approach allows more powerful inferences of natural selection than has previously been possible. We identify multiple regions under strong positive selection, and multi-allelic traits including hair color, body mass index and blood pressure, showing strong evidence of directional selection, varying among human groups.}, }
@article {pmid31475290, year = {2019}, author = {Wang, Q and Zhang, Q and Han, T and Sun, Z and Dechow, PC and Zhu, H and Zhang, Q}, title = {Masticatory properties in pre-modern Holocene populations from Northern China.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {70}, number = {1}, pages = {15-30}, doi = {10.1127/homo/2019/1007}, pmid = {31475290}, issn = {1618-1301}, mesh = {Adult ; Biological Evolution ; Biomechanical Phenomena/physiology ; China ; Female ; Fossils ; History, Ancient ; Humans ; Male ; *Mandible/anatomy &amp; histology/physiology ; Mastication/*physiology ; *Skull/anatomy &amp; histology/physiology ; *Temporomandibular Joint/anatomy &amp; histology/physiology ; *Tooth/anatomy &amp; histology/physiology ; }, abstract = {Recent studies indicate that evolution of the craniofacial skeleton is influenced by dietary behavior, which in turn alters masticatory efficacy and temporomandibular joint (TMJ) stability. In this study the mechanical properties of the masticatory system and the integrity of the TMJ in human populations from Northern China, dated to between 3800 BCE and 100 CE, were assessed. The results demonstrate that the mechanical efficiency is comparable to other modern human populations, though variations are present across different populations. While the ratio of overall weighted muscle efficiency for incisor loading vs. molar loading in pastoral and some recent agricultural groups is similar to early Homo sapiens, the ratio in more ancient agricultural groups is similar to the ratio in populations with heavy anterior paramasticatory activities, such as Neandertals, Inuits, and Native Americans. The TMJ vulnerability negatively correlates with the maxillary dental arch size, and positively with the condylar size. These findings suggest that there are multi-directional strategies in adaptation to heavy anterior teeth loading, such as increasing anterior teeth loading efficiency, increasing facial height, increasing facial breath and facial orthognathy, or decreasing anterior facial length. Furthermore, populations or individuals with a smaller dental arch and high biting efficiency could more easily injure the TMJ during unilateral loadings, which may explain the higher prevalence of TMJ disorders in modern humans, especially in women. These findings further reflect the impact of diachronic changes of the masticatory apparatus and lifestyle and their impact on oral health during recent human history.}, }
@article {pmid33951887, year = {2019}, author = {Caldararo, N}, title = {Probability, Populations, Phylogenetics, and Hominin Speciation.}, journal = {Human biology}, volume = {90}, number = {2}, pages = {129-155}, doi = {10.13110/humanbiology.90.2.04}, pmid = {33951887}, issn = {1534-6617}, abstract = {A number of recent articles have appeared on the hominin Denisova fossil remains. Many of them focus on attempts to produce DNA sequences from the extracted samples. Often these project mitochondrial DNA (mtDNA) sequences from the fossils of a number of Neandertals and the Denisovans in an attempt to understand the evolution of Middle Pleistocene human ancestors. These articles introduce a number of problems in the interpretation of speciation in hominins. One concerns the degradation of the ancient DNA and its interpretation as authentic genetic information. Another problem concerns the ideas of "species" versus "population" and the use of these ideas in building evolutionary diagrams to indicate ancestry and extinction. A third issue concerns the theory of haplotypes in the mtDNA. Given the severe constraints on mutations in the mtDNA genome to maintain functionality and the purifying processes to reduce such mutations in the ovaries, putative geographic and historical variations seem contradictory. Local diversity and variations in supposed "macrohaplotypes" are explained as back migrations or back mutations, which dilutes the robust nature of the theory. A central issue involves what human variation means, how much population variation there has been in the past, and whether this variation distinguishes hominid speciation or is simply a process of anagenesis. This brings up the question of how much can be interpreted from the analysis of DNA. Some businesses today claim to be able to use DNA analysis to discover past ethnic identities, and a new niche in restaurants is producing "DNA" menus. Perhaps some caution is in order.}, }
@article {pmid33951886, year = {2019}, author = {Kislev, M and Barkai, R}, title = {Neanderthal and Woolly Mammoth Molecular Resemblance: Genetic Similarities May Underlie Cold Adaptation Suite.}, journal = {Human biology}, volume = {90}, number = {2}, pages = {115-128}, doi = {10.13110/humanbiology.90.2.03}, pmid = {33951886}, issn = {1534-6617}, abstract = {With the ongoing growth of gene-based research in recent decades, examining changes that have taken place in structures over the course of evolution has become increasingly accessible. One intriguing subject at the forefront of evolutionary research is how environmental pressures affect species evolution through epigenetic adaptation. This article presents the available molecular components of adaptation to cold environments in two extinct mammals: the woolly mammoth and the Neanderthal. These two species coexisted in similar geographic and environmental European settings during the Middle and Upper Pleistocene, and both were direct descendants of African ancestors, although both fully evolved and adapted in Europe during the Middle Pleistocene. The authors assessed the degree of resemblance between mammoth and Neanderthal genetic components by reviewing three case studies of relevant gene variants and alleles associated with cold-climate adaptation found in both genomes. Their observations present the likelihood of a molecular resemblance between the suites of cold adaptation traits in the two species.}, }
@article {pmid31472324, year = {2019}, author = {Barsky, D and Moigne, AM and Pois, V}, title = {The shift from typical Western European Late Acheulian to microproduction in unit 'D' of the late Middle Pleistocene deposits of the Caune de l'Arago (Pyrénées-Orientales, France).}, journal = {Journal of human evolution}, volume = {135}, number = {}, pages = {102650}, doi = {10.1016/j.jhevol.2019.102650}, pmid = {31472324}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Caves ; France ; *Neanderthals ; *Technology ; }, abstract = {Stratigraphic Unit D levels of the Caune de l'Arago (Pyrénées-Orientales, France), situated in the upper part of the depositional sequence of Ensemble Stratigraphique III (ES III), has yielded a rich Acheulian archeopaleontological record dated to the Middle Pleistocene. The site's infill, dated from 690 to 90 ka, encloses a thick cultural sequence comprising some of the oldest evidence of Acheulian documented so far in Western Europe (Unit P levels). The deposits contain successive occupation layers with abundant faunal remains, stone artifacts, and sometimes hominin remains attributed to Homo erectus tautavelensis. The Unit D levels are chronostratigraphically positioned at the top of the ES III sequence, accumulated at the end of Marine Isotope Stage (MIS) 12. The Unit D lithic assemblage shows no evidence of Levallois knapping strategies. Rather, its features indicate a trend towards microproduction that continues into subsequent occupational phases, apparently marking a local expression of the transition from the Lower to the Middle Paleolithic. Remarkably, tiny discoid and multidirectional type cores, predominantly knapped from small-sized quartz pebbles, characterize the Unit D lithic assemblage. Experimental work presented here demonstrates the likelihood that, despite the small size of the cores and the recalcitrant crystalline materials from which they were knapped, flake production can be carried out with free-hand hard hammer techniques. We explore behavioral aspects gleaned from Unit D cultural material, contrasting them with microlithic praxis observed elsewhere in Europe and the Near East in a similar timeframe.}, }
@article {pmid31472033, year = {2019}, author = {Pagano, AS and Márquez, S and Laitman, JT}, title = {Reconstructing the Neanderthal Eustachian Tube: New Insights on Disease Susceptibility, Fitness Cost, and Extinction.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {302}, number = {12}, pages = {2109-2125}, doi = {10.1002/ar.24248}, pmid = {31472033}, issn = {1932-8494}, support = {1128901//Directorate for Social, Behavioral and Economic Sciences/International ; }, mesh = {Adolescent ; Adult ; Animals ; Cartilage/*pathology ; Child ; Disease Susceptibility ; Ear, Middle/*pathology ; Eustachian Tube/*pathology ; *Extinction, Biological ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Neanderthals ; Otitis Media/*pathology ; }, abstract = {Neanderthals are among the best studied and yet most enigmatic fossil human groups with aspects of their anatomy and functional morphology remaining poorly understood. We present the first anatomical reconstruction of the Neanderthal cartilaginous Eustachian tube (CET), a vital component of the upper respiratory tract and nexus for the middle ear and postnasal airway. The Eustachian (auditory, pharyngotympanic) tube, comprised of a bony and cartilaginous (CET) portion, is integral to normal physiological functions such as middle ear aeration and pressure equilibration. Findings indicate that Neanderthal tubal morphology may have predisposed them to high rates of middle ear disease (otitis media [OM]). In living humans, mechanical CET dysfunction underlies OM in infants and young children, with sequelae including hearing loss, meningitis, and pneumonia. Despite proven linkage of CET malfunction with OM, the role of CET morphology in Neanderthal health and disease remains unstudied. We reconstructed Neanderthal CET morphology, comparing their crania to a modern human growth series. Methods included geometric morphometrics and univariate measures among Procrustes-fitted coordinates. Results showed Neanderthal adults exhibiting primitively tall and narrow nasopharynges with infant-like horizontal CET and choanal orientation. As horizontal CET orientation is associated with increased OM incidence in infants and children until around age six, its appearance in Neanderthal adults strongly indicates persistence of high OM susceptibility at this time. This could have compromised fitness and disease load relative to sympatric modern humans, affecting Neanderthals' ability to compete within their ecological niche, and potentially contributing to their rapid extinction. Anat Rec, 302:2109-2125, 2019. © 2019 American Association for Anatomy.}, }
@article {pmid31469987, year = {2019}, author = {Rosandić, M and Vlahović, I and Paar, V}, title = {Novel look at DNA and life-Symmetry as evolutionary forcing.}, journal = {Journal of theoretical biology}, volume = {483}, number = {}, pages = {109985}, doi = {10.1016/j.jtbi.2019.08.016}, pmid = {31469987}, issn = {1095-8541}, mesh = {AT Rich Sequence ; Chromosomes, Human/genetics ; Conserved Sequence ; DNA/*genetics ; Eukaryota/metabolism ; *Evolution, Molecular ; Humans ; Nucleotides/genetics ; Prokaryotic Cells/metabolism ; Symbiosis/genetics ; }, abstract = {After explanation of the Chargaff´s first parity rule in terms of the Watson-Crick base-pairing between the two DNA strands, the Chargaff´s second parity rule for each strand of DNA (also named strand symmetry), which cannot be explained by Watson-Crick base-pairing only, is still a challenging issue already fifty years. We show that during evolution DNA preserves its identity in the form of quadruplet A+T and C+G rich matrices based on purine-pyrimidine mirror symmetries of trinucleotides. Identical symmetries are present in our classification of trinucleotides and the genetic code table. All eukaryotes and almost all prokaryotes (bacteria and archaea) have quadruplet mirror symmetries in structural form and frequencies following the principle of Chargaff's second parity rule and Natural symmetry law of DNA creation and conservation. Some rare symbionts have mirror symmetry only in their structural form within each DNA strand. Based on our matrix analysis of closely related species, humans and Neanderthals, we find that the circular cycle of inverse proportionality between trinucleotides preserves identical relative frequencies of trinucleotides in each quadruplet and in the whole genome. According to our calculations, a change in frequencies in quadruplet matrices could lead to the creation of new species. Violation of quadruplet symmetries is practically inconsistent with life. DNA symmetries provide a key for understanding the restriction of disorder (entropy) due to mutations in the evolution of DNA.}, }
@article {pmid31462783, year = {2019}, author = {Fox, K and Hawks, J}, title = {Use ancient remains more wisely.}, journal = {Nature}, volume = {572}, number = {7771}, pages = {581-583}, pmid = {31462783}, issn = {1476-4687}, mesh = {Animals ; Archaeology/*ethics/*methods ; DNA, Ancient/*analysis/*isolation &amp; purification ; Female ; Genomics/*ethics/*methods ; Hawaii/ethnology ; History, 18th Century ; History, Ancient ; Humans ; Male ; Neanderthals/genetics ; Stakeholder Participation ; }, }
@article {pmid31427508, year = {2019}, author = {Schmidt, P and Blessing, M and Rageot, M and Iovita, R and Pfleging, J and Nickel, KG and Righetti, L and Tennie, C}, title = {Birch tar production does not prove Neanderthal behavioral complexity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {36}, pages = {17707-17711}, pmid = {31427508}, issn = {1091-6490}, mesh = {Animals ; *Archaeology ; Behavior, Animal/*physiology ; *Betula ; Cognition/*physiology ; Neanderthals/*physiology ; }, abstract = {Birch tar production by Neanderthals-used for hafting tools-has been interpreted as one of the earliest manifestations of modern cultural behavior. This is because birch tar production per se was assumed to require a cognitively demanding setup, in which birch bark is heated in anaerobic conditions, a setup whose inherent complexity was thought to require modern levels of cognition and cultural transmission. Here we demonstrate that recognizable amounts of birch tar were likely a relatively frequent byproduct of burning birch bark (a natural tinder) under common, i.e., aerobic, conditions. We show that when birch bark burns close to a vertical to subvertical hard surface, such as an adjacent stone, birch tar is naturally deposited and can be easily scraped off the surface. The burning of birch bark near suitable surfaces provides useable quantities of birch tar in a single work session (3 h; including birch bark procurement). Chemical analysis of the resulting tar showed typical markers present in archaeological tar. Mechanical tests verify the tar's suitability for hafting and for hafted tools use. Given that similarly sized stones as in our experiment are frequently found in archaeological contexts associated with Neanderthals, the cognitively undemanding connection between burning birch bark and the production of birch tar would have been readily discoverable multiple times. Thus, the presence of birch tar alone cannot indicate the presence of modern cognition and/or cultural behaviors in Neanderthals.}, }
@article {pmid31421316, year = {2019}, author = {Zanolli, C and Biglari, F and Mashkour, M and Abdi, K and Monchot, H and Debue, K and Mazurier, A and Bayle, P and Le Luyer, M and Rougier, H and Trinkaus, E and Macchiarelli, R}, title = {A Neanderthal from the Central Western Zagros, Iran. Structural reassessment of the Wezmeh 1 maxillary premolar.}, journal = {Journal of human evolution}, volume = {135}, number = {}, pages = {102643}, doi = {10.1016/j.jhevol.2019.102643}, pmid = {31421316}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Bicuspid/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Iran ; Maxilla ; Neanderthals/*anatomy &amp; histology ; }, abstract = {Wezmeh Cave, in the Kermanshah region of Central Western Zagros, Iran, produced a Late Pleistocene faunal assemblage rich in carnivorans along with a human right maxillary premolar, Wezmeh 1, an unerupted tooth from an 8 ± 2 year-old individual. Uranium-series analyses of the fauna by alpha spectrometry provided age estimates between 70 and 11 ka. Crown dimensions place the tooth specimen at the upper limits of Late Pleistocene human ranges of variation. Wezmeh 1 metameric position (most likely a P[3]) remains uncertain and only its surficial morphology has been described so far. Accordingly, we used microfocus X-ray tomography (12.5 μm isotropic voxel size) to reassess the metameric position and taxonomic attribution of this specimen. We investigated its endostructural features and quantified crown tissue proportions. Topographic maps of enamel thickness (ET) distribution were also generated, and semilandmark-based geometric morphometric analyses of the enamel-dentine junction (EDJ) were performed. We compared Wezmeh 1 with unworn/slightly-moderately worn P[3] and P[4] of European Neanderthals, Middle Paleolithic modern humans from Qafzeh, an Upper Paleolithic premolar, and Holocene humans. The results confirm that Wezmeh 1 represents a P[3]. Based on its internal conformation and especially EDJ shape, Wezmeh 1 aligns closely with Neanderthals and is distinct from the fossil and extant modern human pattern of our comparative samples. Wezmeh 1 is thus the first direct evidence of Neanderthal presence on the western margin of the Iranian Plateau.}, }
@article {pmid31412053, year = {2019}, author = {Trinkaus, E and Samsel, M and Villotte, S}, title = {External auditory exostoses among western Eurasian late Middle and Late Pleistocene humans.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0220464}, pmid = {31412053}, issn = {1932-6203}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; Ear Diseases/*pathology ; Exostoses/*pathology ; Fossils ; Humans ; Neanderthals ; }, abstract = {External auditory exostoses (EAE) have been noted among the Neandertals and a few other Pleistocene humans, but until recently they have been discussed primary as minor pathological lesions with possible auditory consequences. An assessment of available western Eurasian late Middle and Late Pleistocene human temporal bones with sufficiently preserved auditory canals (n = 77) provides modest levels of EAE among late Middle Pleistocene archaic humans (≈20%) and early modern humans (Middle Paleolithic: ≈25%; Early/Mid Upper Paleolithic: 20.8%; Late Upper Paleolithic: 9.5%). The Neandertals, however, exhibit an exceptionally high level of EAE (56.5%; 47.8% if two anomalous cases are considered normal). The levels of EAE for the early modern humans are well within recent human ranges of variation, frequencies which are low for equatorial inland and high latitude samples but occasionally higher elsewhere. The Early/Mid Upper Paleolithic frequency is nonetheless high for a high latitude sample under interpleniglacial conditions. Given the strong etiological and environmental associations of EAE development with exposure to cold water and/or damp wind chill, the high frequency of EAE among the Neandertals implies frequent aquatic resource exploitation, more frequent than the archeological and stable isotopic evidence for Middle Paleolithic/Neandertal littoral and freshwater resource foraging implies. As such, the Neandertal data parallel a similar pattern evident in eastern Eurasian archaic humans. Yet, factors in addition to cold water/wind exposure may well have contributed to their high EAE frequencies.}, }
@article {pmid31409814, year = {2019}, author = {Zwyns, N and Paine, CH and Tsedendorj, B and Talamo, S and Fitzsimmons, KE and Gantumur, A and Guunii, L and Davakhuu, O and Flas, D and Dogandžić, T and Doerschner, N and Welker, F and Gillam, JC and Noyer, JB and Bakhtiary, RS and Allshouse, AF and Smith, KN and Khatsenovich, AM and Rybin, EP and Byambaa, G and Hublin, JJ}, title = {The Northern Route for Human dispersal in Central and Northeast Asia: New evidence from the site of Tolbor-16, Mongolia.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11759}, pmid = {31409814}, issn = {2045-2322}, mesh = {Animals ; Asia ; Fossils ; *Human Migration ; Humans ; Mongolia ; Neanderthals/*genetics ; }, abstract = {The fossil record suggests that at least two major human dispersals occurred across the Eurasian steppe during the Late Pleistocene. Neanderthals and Modern Humans moved eastward into Central Asia, a region intermittently occupied by the enigmatic Denisovans. Genetic data indicates that the Denisovans interbred with Neanderthals near the Altai Mountains (South Siberia) but where and when they met H. sapiens is yet to be determined. Here we present archaeological evidence that document the timing and environmental context of a third long-distance population movement in Central Asia, during a temperate climatic event around 45,000 years ago. The early occurrence of the Initial Upper Palaeolithic, a techno-complex whose sudden appearance coincides with the first occurrence of H. sapiens in the Eurasian steppes, establishes an essential archaeological link between the Siberian Altai and Northwestern China . Such connection between regions provides empirical ground to discuss contacts between local and exogenous populations in Central and Northeast Asia during the Late Pleistocene.}, }
@article {pmid31392716, year = {2019}, author = {Garralda, MD and Maíllo-Fernández, JM and Higham, T and Neira, A and Bernaldo de Quirós, F}, title = {The Gravettian child mandible from El Castillo Cave (Puente Viesgo, Cantabria, Spain).}, journal = {American journal of physical anthropology}, volume = {170}, number = {3}, pages = {331-350}, doi = {10.1002/ajpa.23906}, pmid = {31392716}, issn = {1096-8644}, support = {HAR2015-70652-P//Spanish Ministry of Research and Science/International ; HAR2012-35214//Spanish Ministry of Research and Science/International ; }, mesh = {Anthropology, Physical ; Caves ; Child, Preschool ; *Fossils ; History, Ancient ; Humans ; Male ; Mandible/*anatomy &amp; histology/*chemistry ; Radiometric Dating ; Spain ; Tooth/anatomy &amp; histology/chemistry ; }, abstract = {OBJECTIVES: This article documents an incomplete child's mandible found in H. Obermaier's excavation campaign (in 1912) in El Castillo Cave, Spain. This fossil was assigned to what was then considered a phase of the "Aurignacian-delta".<br><br>MATERIALS AND METHODS: We exhaustively analyzed the original Obermaier documents, with particular attention to those corresponding to the year of the discovery. We extracted a bone sample to radiocarbon date the fossil directly. We also followed established methods to measure, describe and compare the mandible with other human remains.<br><br>RESULTS: The analysis of Obermaier's documents and new data derived from modern excavations, show that the mandible was discovered in an interior area of the cave. Direct radiocarbon dating yielded a result of 24,720&#x2009;&#xb1;&#x2009;210 BP and 29,300 - 28,300&#x2009;cal BP, a date similar to those known for the Gravettian technocomplex both in the El Castillo site and across Europe. The jaw corresponded to a child aged 4-5 years, with modern morphology, but with a certain robustness, especially in the symphyseal region. Comparisons were made with several modern children (Granada, Spitalfields, and Black series) and with immature fossils (European Aurignacian and Gravettian). The few differences between the modern and the fossil children are related to the symphysis and mandibular corpus thickness and height, and to the symphyseal morphology and larger teeth dimensions. Paleoisotopic data for Castillo C correspond with a varied diet. Numerous cutmarks were identified in the midline internal symphyseal region.<br><br>DISCUSSION AND CONCLUSIONS: The results agree with those published for other fossils of similar age and chronology (e.g., the mandible of the Lagar Velho child) and show clear differences from the jaws of the young Neanderthals. The interpretation of the original data on the mandible discovery may indicate the destruction of a burial and the displacement, by percolation or by a den, at least of part of the skeleton. The perimortem manipulations in the child's mandible are the first described in the Gravettian world of Western Europe.}, }
@article {pmid31386798, year = {2020}, author = {Mikaeeli, S and Susan-Resiga, D and Girard, E and Ben Djoudi Ouadda, A and Day, R and Prost, S and Seidah, NG}, title = {Functional analysis of natural PCSK9 mutants in modern and archaic humans.}, journal = {The FEBS journal}, volume = {287}, number = {3}, pages = {515-528}, doi = {10.1111/febs.15036}, pmid = {31386798}, issn = {1742-4658}, support = {148363//CIHR/Canada ; }, mesh = {Animals ; Binding Sites ; DNA Methylation ; Humans ; *Loss of Function Mutation ; Neanderthals/*genetics ; Proprotein Convertase 9/chemistry/*genetics/metabolism ; Protein Binding ; Receptors, LDL/metabolism ; }, abstract = {PCSK9 is the last member of the proprotein convertases (PCs) family and its gene is mutated in ~ 2% to 3% of individuals with familial hypercholesterolemia (FH). This protein enhances the degradation of the low-density lipoprotein receptor (LDLR) and hence increases the levels of circulating LDL-cholesterol (LDLc). Studies of the underlying mechanism(s) regulating the activity of different mutations in the PCSK9 gene are ongoing as they enhance our understanding of the biology and clinical relevance of PCSK9 and its partners. In an attempt to unravel the regulation of PCSK9 transcription and possibly identify mutation 'hot spot' regions with alterations in CpG methylation, we present for the first time the complete methylome profile of the PCSK9 gene in modern and archaic humanoids. Our data showed that the genomes of modern humans and archaic PCSK9 exhibit a similar methylation pattern. Next, we defined the mechanistic consequences of three PCSK9 natural mutations (PCSK9-R96L, -R105W, and -P174S) and one archaic Denisovan mutation (PCSK9-H449L) using various complementary cellular and in vitro binding assays. Our results showed that the PCSK9-H449L is a loss-of-function (LOF) mutation, likely due to its lower binding affinity to the LDLR. Similarly, PCSK9-R96L and -R105W are LOF mutations, even though they have been identified in FH patients. The PCSK9-R105W mutation leads to a significantly lower autocatalytic processing of proPCSK9. PCSK9-P174S resulted in a LOF in both extracellular and intracellular pathways. In conclusion, our extensive analyses revealed that all studied mutations result in PCSK9 LOF, via various mechanisms, leading to lower levels of LDLc.}, }
@article {pmid31368158, year = {2019}, author = {Lieberman, P}, title = {The antiquity and evolution of the neural bases of rhythmic activity.}, journal = {Annals of the New York Academy of Sciences}, volume = {1453}, number = {1}, pages = {114-124}, doi = {10.1111/nyas.14199}, pmid = {31368158}, issn = {1749-6632}, mesh = {Animals ; *Biological Evolution ; Brain/*physiology ; Humans ; *Language ; Larynx/physiology ; *Periodicity ; Speech/*physiology ; Vocal Cords/physiology ; }, abstract = {The evolution of the anatomy and neural circuits that regulate the rhythm of speech can be traced back to the Devonian age, 400 million years ago. Epigenetic processes 100 million years later modified these circuits. Natural selection on similar genetic processes occurred during the evolution of archaic hominins and humans. The lungs and larynx-anatomy that produces the rhythmic fundamental frequency patterns of speech-have a deep evolutionary history. Neural circuits linking the cortex, basal ganglia, and other subcortical structures plan, sequence, and execute motor as well as cognitive acts. These neural circuits generate the rhythm of speech, singing, and chanting. The human form of the transcription factor FOXP2 increased synaptic connectivity and plasticity in basal ganglia circuits, enhancing motor control and cognitive and linguistic capabilities in humans as well as Neanderthals. The archeological record also suggests that Neanderthals passed spoken language. Homologous circuits existed in amphibians. In songbirds, the avian form of FOXP2 acted on similar neural circuits allowing birds to learn and produce new songs. Current studies point to natural selection on genetic events enhancing these and other neural circuits to yield fully human rhythmic speech, and motor, cognitive, and linguistic capabilities, rather than the saltation proposed by Noam Chomsky.}, }
@article {pmid31358183, year = {2019}, author = {Aranguren, B and Grimaldi, S and Benvenuti, M and Capalbo, C and Cavanna, F and Cavulli, F and Ciani, F and Comencini, G and Giuliani, C and Grandinetti, G and Mariotti Lippi, M and Masini, F and Mazza, PPA and Pallecchi, P and Santaniello, F and Savorelli, A and Revedin, A}, title = {Poggetti Vecchi (Tuscany, Italy): A late Middle Pleistocene case of human-elephant interaction.}, journal = {Journal of human evolution}, volume = {133}, number = {}, pages = {32-60}, doi = {10.1016/j.jhevol.2019.05.013}, pmid = {31358183}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; *Elephants ; *Food Chain ; Fossils ; Italy ; *Neanderthals ; Paleontology ; *Tool Use Behavior ; }, abstract = {A paleosurface with a concentration of wooden-, bone-, and stone-tools interspersed among an accumulation of fossil bones, largely belonging to the straight-tusked elephant Palaeoloxodon antiquus, was found at the bottom of a pool, fed by hot springs, that was excavated at Poggetti Vecchi, near Grosseto (Tuscany, Italy). The site is radiometrically dated to the late Middle Pleistocene, around 171,000 years BP. Notable is the association of the artifacts with the elephant bones, and in particular the presence of digging sticks made from boxwood (Buxus sp.). Although stone tools show evidence of use mainly on animal tissues, indicating some form of interaction between hominins and animals, the precise use of the sticks is unclear. Here we discuss about the role played by the hominins at the site: paleobiological and taphonomic evidence indicates that the elephants died by a natural cause and were butchered soon after their death. The associated paleontological and archeological evidence from this site provides fresh insights into the behavior of early Neanderthals in Central Italy. The discovery of Poggetti Vecchi shows how opportunistically flexible Neanderthals were in response to environmental contingencies.}, }
@article {pmid31358180, year = {2019}, author = {Davies, TW and Delezene, LK and Gunz, P and Hublin, JJ and Skinner, MM}, title = {Endostructural morphology in hominoid mandibular third premolars: Geometric morphometric analysis of dentine crown shape.}, journal = {Journal of human evolution}, volume = {133}, number = {}, pages = {198-213}, doi = {10.1016/j.jhevol.2019.06.004}, pmid = {31358180}, issn = {1095-8606}, mesh = {Animals ; Bicuspid/*anatomy &amp; histology ; Dentin/*anatomy &amp; histology ; Fossils/anatomy &amp; histology ; Hominidae/*anatomy &amp; histology ; Mandible ; Species Specificity ; Tooth Crown/*anatomy &amp; histology ; }, abstract = {In apes, the mandibular third premolar (P3) is adapted for a role in honing the large upper canine. The role of honing was lost early in hominin evolution, releasing the tooth from this functional constraint and allowing it to respond to subsequent changes in masticatory demands. This led to substantial morphological changes, and as such the P3 has featured prominently in systematic analyses of the hominin clade. The application of microtomography has also demonstrated that examination of the enamel-dentine junction (EDJ) increases the taxonomic value of variations in crown morphology. Here we use geometric morphometric techniques to analyze the shape of the P3 EDJ in a broad sample of fossil hominins, modern humans, and extant apes (n = 111). We test the utility of P3 EDJ shape for distinguishing among hominoids, address the affinities of a number of hominin specimens of uncertain taxonomic attribution, and characterize the changes in P3 EDJ morphology across our sample, with particular reference to features relating to canine honing and premolar 'molarization'. We find that the morphology of the P3 EDJ is useful in taxonomic identification of individual specimens, with a classification accuracy of up to 88%. The P3 EDJ of canine-honing apes displays a tall protoconid, little metaconid development, and an asymmetrical crown shape. Plio-Pleistocene hominin taxa display derived masticatory adaptations at the EDJ, such as the molarized premolars of Australopithecus africanus and Paranthropus, which have well-developed marginal ridges, an enlarged talonid, and a large metaconid. Modern humans and Neanderthals display a tall dentine body and reduced metaconid development, a morphology shared with premolars from Mauer and the Cave of Hearths. Homo naledi displays a P3 EDJ morphology that is unique among our sample; it is quite unlike Middle Pleistocene and recent Homo samples and most closely resembles Australopithecus, Paranthropus and early Homo specimens.}, }
@article {pmid31358177, year = {2019}, author = {Richard, M and Falguères, C and Valladas, H and Ghaleb, B and Pons-Branchu, E and Mercier, N and Richter, D and Conard, NJ}, title = {New electron spin resonance (ESR) ages from Geißenklösterle Cave: A chronological study of the Middle and early Upper Paleolithic layers.}, journal = {Journal of human evolution}, volume = {133}, number = {}, pages = {133-145}, doi = {10.1016/j.jhevol.2019.05.014}, pmid = {31358177}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; *Caves ; Dental Enamel/*chemistry ; *Electron Spin Resonance Spectroscopy ; *Fossils ; Germany ; Humans ; *Neanderthals ; }, abstract = {Geißenklösterle Cave (Germany) is one of the most important Paleolithic sites in Europe, as it is characterized by human occupation during the Middle and early Upper Paleolithic. Aurignacian layers prior to 37-38 ka cal BP feature both musical and figurative art objects that are linked to the early arrival in Europe of Homo sapiens. Middle Paleolithic layers yielded lithic artifacts attributed to Homo neanderthalensis. Since human occupation at the site is attributed to both Neanderthals and modern humans, chronology is essential to clarify the issues of Neanderthal disappearance, modern human expansion in Europe, and the origin of the Aurignacian in Western Europe. Electron spin resonance (ESR) dating was performed on fossil tooth enamel collected from the Middle Paleolithic layers, which are beyond the radiocarbon dating range, and from the nearly sterile 'transitional' geological horizon (GH) 17 and the lower Aurignacian deposits, to cross-check ESR ages with previous radiocarbon, thermoluminescence and ESR age results. The Middle Paleolithic layers were dated between 94 ± 10 ka (GH 21) and 55 ± 6 ka (GH 18) by ESR on tooth enamel. Mean ages for GH 17, at 46 ± 3 ka, and for the lower Aurignacian layers, at 37 ± 3 ka, are in agreement with previous dating results, thus supporting the reliability of ESR chronology for the base of the sequence where dating comparisons are not possible. These results suggest that Neanderthals occupied the site from Marine Isotope Stage (MIS) 5 to the second half of MIS 3 and confirm the antiquity of early Aurignacian deposits. The presence of an almost sterile layer that separates Middle and Upper Paleolithic occupations could be related to the abandonment of the site by Neanderthals, possibly during Heinrich Stadial 5 (ca. 49-47 ka), thus before the arrival of H. sapiens in the area around 42 ka cal BP. These dates for the Middle Paleolithic of the Swabian Jura represent an important contribution to the prehistory of the region, where nearly all of the excavations were conducted decades ago and prior to the development of reliable radiometric dating beyond the range of radiocarbon.}, }
@article {pmid31341308, year = {2019}, author = {El-Showk, S}, title = {Neanderthal clues to brain evolution in humans.}, journal = {Nature}, volume = {571}, number = {7766}, pages = {S10-S11}, pmid = {31341308}, issn = {1476-4687}, mesh = {Animals ; Brain ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; }, }
@article {pmid31336034, year = {2020}, author = {Bräuer, G and Pitsios, T and Säring, D and von Harling, M and Jessen, F and Kroll, A and Groden, C}, title = {Virtual Reconstruction and Comparative Analyses of the Middle Pleistocene Apidima 2 Cranium (Greece).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {303}, number = {5}, pages = {1374-1392}, doi = {10.1002/ar.24225}, pmid = {31336034}, issn = {1932-8494}, mesh = {Animals ; Biological Evolution ; *Fossils ; Greece ; Hominidae/*anatomy &amp; histology ; Image Processing, Computer-Assisted ; Neanderthals/anatomy &amp; histology ; Skull/*anatomy &amp; histology/diagnostic imaging ; }, abstract = {The Apidima 2 fossil cranium from South Peloponnese is one of the most important hominin specimens from Southeast Europe. Nevertheless, there has been continuous controversy as to whether it represents a so-called Preneandertal/Homo heidelbergensis such as, for example, the Petralona cranium from Northern Greece or a more derived Neandertal. Recent absolute dating evidence alone cannot clarify the issue because both classifications would be possible during the respective Middle Pleistocene time span. Since only limited data were available on the cranium, there have been repeated claims for the need of a broader comparative study of the hominin. The present article presents a CT-based virtual reconstruction including corrections of postmortem fractures and deformation as well as detailed metrical and morphological analyses of the specimen. Endocranial capacity could be estimated for the first time based on virtual reconstruction. Our multivariate analyses of metric data from the face and vault revealed close affinities to early and later Neandertals, especially showing the derived facial morphometrics. In addition, comparative analyses of Apidima 2 were done for many derived Neandertal features. Here again, a significant number of Neandertal features could be found in the Apidima cranium but no conditions common in Preneandertals. In agreement with a later Middle Pleistocene age Apidima is currently the earliest evidence of a hominin in Europe with such a derived Neandertal facial morphology. The place of Apidima in the complex process of Neandertal evolution as well as its taxonomic classification are discussed as well. Anat Rec, 303:1374-1392, 2020. © 2019 American Association for Anatomy.}, }
@article {pmid31314755, year = {2019}, author = {Pitarch Martí, A and d'Errico, F and Turq, A and Lebraud, E and Discamps, E and Gravina, B}, title = {Provenance, modification and use of manganese-rich rocks at Le Moustier (Dordogne, France).}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0218568}, pmid = {31314755}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; *Fossils ; France ; History, Ancient ; Humans ; *Manganese ; *Minerals ; *Neanderthals ; Technology/*history ; }, abstract = {The use of colouring materials by Neanderthals has attracted a great deal of attention in recent years. Here we present a taphonomic, technological, chemical-mineralogical and functional analysis of fifty-four manganese rich lumps recovered during past and on-going excavations at the lower rockshelter of Le Moustier (Dordogne, France). We compare compositional data for archaeological specimens with the same information for twelve potential geological sources. Morphometric analysis shows that material from Peyrony's excavations before the First World War provides a highly biased picture of the importance of these materials for Mousterian groups. These early excavations almost exclusively recovered large modified pieces, while Mn-rich lumps from the on-going excavations predominantly consist of small pieces, only half of which bear traces of modification. We estimate that at least 168 pieces were not recovered during early work at the site. Neanderthals developed a dedicated technology for processing Mn-rich fragments, which involved a variety of tools and motions. Processing techniques were adapted to the size and density of the raw material, and evidence exists for the successive or alternating use of different techniques. Morphological, textural and chemical differences between geological and archaeological samples suggest that Neanderthals did not collect Mn-rich lumps at the outcrops we sampled. The association and variability in Mn, Ni, As, Ba content, compared to that observed at the sampled outcrops, suggests that either the Le Moustier lumps come from a unique source with a broad variation in composition, associating Mn, Ni, As, Ba, or that they were collected at different sources, characterized either by Mn-Ni-As or Mn-Ba. In the latter case, changes in raw material composition across the stratigraphy support the idea that Neanderthal populations bearing different stone tool technologies collected Mn fragments from different outcrops. Our results favour a use of these materials for multiple utilitarian and symbolic purposes.}, }
@article {pmid31308224, year = {2019}, author = {Bokelmann, L and Hajdinjak, M and Peyrégne, S and Brace, S and Essel, E and de Filippo, C and Glocke, I and Grote, S and Mafessoni, F and Nagel, S and Kelso, J and Prüfer, K and Vernot, B and Barnes, I and Pääbo, S and Meyer, M and Stringer, C}, title = {A genetic analysis of the Gibraltar Neanderthals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {31}, pages = {15610-15615}, pmid = {31308224}, issn = {1091-6490}, support = {100713/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *DNA, Ancient ; Gibraltar ; History, Ancient ; Humans ; Neanderthals/*genetics ; *Oligonucleotide Array Sequence Analysis ; }, abstract = {The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.}, }
@article {pmid31300536, year = {2019}, author = {Teixeira, JC and Cooper, A}, title = {Using hominin introgression to trace modern human dispersals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {31}, pages = {15327-15332}, pmid = {31300536}, issn = {1091-6490}, mesh = {Africa ; Animals ; Asia, Southeastern ; DNA/genetics ; Geography ; Hominidae/*physiology ; *Human Migration ; Humans ; Population Dynamics ; }, abstract = {The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace's Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.}, }
@article {pmid31296750, year = {2019}, author = {Wade, L}, title = {Was our species in Europe 210,000 years ago?.}, journal = {Science (New York, N.Y.)}, volume = {365}, number = {6449}, pages = {111}, doi = {10.1126/science.365.6449.111}, pmid = {31296750}, issn = {1095-9203}, mesh = {Animals ; Anthropology ; Caves ; *Extinction, Biological ; Fossils/anatomy &amp; histology ; Greece ; Humans ; Neanderthals/*anatomy &amp; histology ; Skull/*anatomy &amp; histology ; }, }
@article {pmid31292546, year = {2019}, author = {Harvati, K and Röding, C and Bosman, AM and Karakostis, FA and Grün, R and Stringer, C and Karkanas, P and Thompson, NC and Koutoulidis, V and Moulopoulos, LA and Gorgoulis, VG and Kouloukoussa, M}, title = {Apidima Cave fossils provide earliest evidence of Homo sapiens in Eurasia.}, journal = {Nature}, volume = {571}, number = {7766}, pages = {500-504}, pmid = {31292546}, issn = {1476-4687}, mesh = {Animals ; Biological Evolution ; *Caves ; *Fossils ; Greece ; Humans ; Neanderthals/anatomy &amp; histology/classification ; Principal Component Analysis ; Radiometric Dating ; Skull/*anatomy &amp; histology ; Time Factors ; }, abstract = {Two fossilized human crania (Apidima 1 and Apidima 2) from Apidima Cave, southern Greece, were discovered in the late 1970s but have remained enigmatic owing to their incomplete nature, taphonomic distortion and lack of archaeological context and chronology. Here we virtually reconstruct both crania, provide detailed comparative descriptions and analyses, and date them using U-series radiometric methods. Apidima 2 dates to more than 170 thousand years ago and has a Neanderthal-like morphological pattern. By contrast, Apidima 1 dates to more than 210 thousand years ago and presents a mixture of modern human and primitive features. These results suggest that two late Middle Pleistocene human groups were present at this site-an early Homo sapiens population, followed by a Neanderthal population. Our findings support multiple dispersals of early modern humans out of Africa, and highlight the complex demographic processes that characterized Pleistocene human evolution and modern human presence in southeast Europe.}, }
@article {pmid31278514, year = {2019}, author = {Brzozowska, MM and Havula, E and Allen, RB and Cox, MP}, title = {Genetics, adaptation to environmental changes and archaic admixture in the pathogenesis of diabetes mellitus in Indigenous Australians.}, journal = {Reviews in endocrine &amp; metabolic disorders}, volume = {20}, number = {3}, pages = {321-332}, pmid = {31278514}, issn = {1573-2606}, mesh = {Australia ; Diabetes Mellitus, Type 2/*genetics/*pathology ; Genome-Wide Association Study ; Humans ; Indigenous Peoples ; Obesity/genetics/pathology ; }, abstract = {Indigenous Australians are particularly affected by type 2 diabetes mellitus (T2D) due to both their genetic susceptibility and a range of environmental and lifestyle risk factors. Recent genetic studies link predisposition to some diseases, including T2D, to alleles acquired from archaic hominins, such as Neanderthals and Denisovans, which persist in the genomes of modern humans today. Indo-Pacific human populations, including Indigenous Australians, remain extremely underrepresented in genomic research with a paucity of data examining the impact of Denisovan or Neanderthal lineages on human phenotypes in Oceania. The few genetic studies undertaken emphasize the uniqueness and antiquity of Indigenous Australian genomes, with possibly the largest proportion of Denisovan ancestry of any population in the world. In this review, we focus on the potential contributions of ancient genes/pathways to modern human phenotypes, while also highlighting the evolutionary roles of genetic adaptation to dietary and environmental changes associated with an adopted Western lifestyle. We discuss the role of genetic and epigenetic factors in the pathogenesis of T2D in understudied Indigenous Australians, including the potential impact of archaic gene lineages on this disease. Finally, we propose that greater understanding of the underlying genetic predisposition may contribute to the clinical efficacy of diabetes management in Indigenous Australians. We suggest that improved identification of T2D risk variants in Oceania is needed. Such studies promise to clarify how genetic and phenotypic differences vary between populations and, crucially, provide novel targets for personalised medical therapies in currently marginalized groups.}, }
@article {pmid31276507, year = {2019}, author = {Centi, L and Groman-Yaroslavski, I and Friedman, N and Oron, M and Prévost, M and Zaidner, Y}, title = {The bulb retouchers in the Levant: New insights into Middle Palaeolithic retouching techniques and mobile tool-kit composition.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0218859}, pmid = {31276507}, issn = {1932-6203}, mesh = {Animals ; Archaeology/*methods ; Bone and Bones/*anatomy &amp; histology ; *Fossils ; Geography ; Humans ; Mediterranean Region ; *Neanderthals ; Problem Solving/physiology ; Time Factors ; Tool Use Behavior/physiology ; }, abstract = {In this paper we describe two assemblages of flint retouchers or "bulb retouchers" retrieved from Nesher Ramla and Quneitra, two Middle Palaeolithic, open-air sites in the Levant. The site of Nesher Ramla yielded the largest assemblage of bulb retouchers (n = 159) currently known, allowing a detailed investigation of this poorly known phenomenon. An extensive experimental program and use-wear analysis enabled us to characterize the different sets of traces related to the retouching activity and to identify different motions applied by the knappers in the course of this action. In both sites, blanks used as bulb retouchers were almost exclusively retouched items, with a special emphasis on convergent morphotypes in Nesher Ramla. The use of retouched items as bulb retouchers is a common trait over different time spans and geographical areas. Our data suggests that bulb retouchers were versatile, multi-purpose tools with a long use-life, transported over long distances as components of the hunter-gatherer mobile tool kit. The high frequencies of bulb retouchers within some archaeological units of Nesher Ramla appear to be connected to the highly curated nature of the lithic assemblages, in turn reflecting a high mobility of the human groups that produced them.}, }
@article {pmid31258332, year = {2019}, author = {Williams, AC and Hill, LJ}, title = {Nicotinamide as Independent Variable for Intelligence, Fertility, and Health: Origin of Human Creative Explosions?.}, journal = {International journal of tryptophan research : IJTR}, volume = {12}, number = {}, pages = {1178646919855944}, pmid = {31258332}, issn = {1178-6469}, abstract = {Meat and nicotinamide acquisition was a defining force during the 2-million-year evolution of the big brains necessary for, anatomically modern, Homo sapiens to survive. Our next move was down the food chain during the Mesolithic 'broad spectrum', then horticultural, followed by the Neolithic agricultural revolutions and progressively lower average 'doses' of nicotinamide. We speculate that a fertility crisis and population bottleneck around 40 000 years ago, at the time of the Last Glacial Maximum, was overcome by Homo (but not the Neanderthals) by concerted dietary change plus profertility genes and intense sexual selection culminating in behaviourally modern Homo sapiens. Increased reliance on the 'de novo' synthesis of nicotinamide from tryptophan conditioned the immune system to welcome symbionts, such as TB (that excrete nicotinamide), and to increase tolerance of the foetus and thereby fertility. The trade-offs during the warmer Holocene were physical and mental stunting and more infectious diseases and population booms and busts. Higher nicotinamide exposure could be responsible for recent demographic and epidemiological transitions to lower fertility and higher longevity, but with more degenerative and auto-immune disease.}, }
@article {pmid31249872, year = {2019}, author = {Peyrégne, S and Slon, V and Mafessoni, F and de Filippo, C and Hajdinjak, M and Nagel, S and Nickel, B and Essel, E and Le Cabec, A and Wehrberger, K and Conard, NJ and Kind, CJ and Posth, C and Krause, J and Abrams, G and Bonjean, D and Di Modica, K and Toussaint, M and Kelso, J and Meyer, M and Pääbo, S and Prüfer, K}, title = {Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe.}, journal = {Science advances}, volume = {5}, number = {6}, pages = {eaaw5873}, pmid = {31249872}, issn = {2375-2548}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Cell Lineage/genetics ; Cell Nucleus/*genetics ; DNA/*genetics ; Europe ; Evolution, Molecular ; Fossils ; Genome/genetics ; Germany ; Mitochondria/genetics ; Neanderthals/*genetics ; }, abstract = {Little is known about the population history of Neandertals over the hundreds of thousands of years of their existence. We retrieved nuclear genomic sequences from two Neandertals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago. Despite the deeply divergent mitochondrial lineage present in the former individual, both Neandertals are genetically closer to later Neandertals from Europe than to a roughly contemporaneous individual from Siberia. That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neandertals suggests that all later Neandertals trace at least part of their ancestry back to these early European Neandertals.}, }
@article {pmid31242180, year = {2019}, author = {Ekshtain, R and Malinsky-Buller, A and Greenbaum, N and Mitki, N and Stahlschmidt, MC and Shahack-Gross, R and Nir, N and Porat, N and Bar-Yosef Mayer, DE and Yeshurun, R and Been, E and Rak, Y and Agha, N and Brailovsky, L and Krakovsky, M and Spivak, P and Ullman, M and Vered, A and Barzilai, O and Hovers, E}, title = {Persistent Neanderthal occupation of the open-air site of 'Ein Qashish, Israel.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0215668}, pmid = {31242180}, issn = {1932-6203}, mesh = {Animals ; Fossils/*anatomy &amp; histology ; Israel ; Mollusca/anatomy &amp; histology/classification ; Neanderthals/*anatomy &amp; histology ; }, abstract = {Over the last two decades, much of the recent efforts dedicated to the Levantine Middle Paleolithic has concentrated on the role of open-air sites in the settlement system in the region. Here focus on the site of 'Ein Qashish as a cases study. Located in present-day northern Israel, the area of this site is estimated to have been >1300 m2, of which ca. 670 were excavated. The site is located at the confluence of the Qishon stream with a small tributary running off the eastern flanks of the Mt. Carmel. At the area of this confluence, water channels and alluvial deposits created a dynamic depositional environment. Four Archaeological Units were identified in a 4.5-m thick stratigraphic sequence were dated by Optically Stimulated Luminescence (OSL) to between-71 and 54 ka, and probably shorter time span-~70-~60 ka. Here we present the diverse material culture remains from the site (lithics, including refitted sequences; modified limestone pieces; molluscs; faunal remains) against their changing paleogeographic backdrop. Skeletal evidence suggests that these remains were associated with Neanderthals. The large-scale repeated accumulation of late Middle Paleolithic remains in the same place on the landscape provides a unique opportunity to address questions of occupation duration and intensity in open-air sites. We find that each occupation was of ephemeral nature, yet presents a range of activities, suggesting that the locale has been used as a generalized residential site rather than specialized task-specific ones. This role of 'Ein Qashish did not change through time, suggesting that during the late Middle Paleolithic settlement system in this part of the southern Levant were stable.}, }
@article {pmid31237235, year = {2019}, author = {Langley, SA and Miga, KH and Karpen, GH and Langley, CH}, title = {Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31237235}, issn = {2050-084X}, support = {R01 GM117420/GM/NIGMS NIH HHS/United States ; R01 GM119011/GM/NIGMS NIH HHS/United States ; }, mesh = {*Centromere ; *Chromosomes, Human ; DNA, Satellite/genetics ; *Genetic Variation ; *Haplotypes ; Humans ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Despite critical roles in chromosome segregation and disease, the repetitive structure and vast size of centromeres and their surrounding heterochromatic regions impede studies of genomic variation. Here we report the identification of large-scale haplotypes (cenhaps) in humans that span the centromere-proximal regions of all metacentric chromosomes, including the arrays of highly repeated α-satellites on which centromeres form. Cenhaps reveal deep diversity, including entire introgressed Neanderthal centromeres and equally ancient lineages among Africans. These centromere-spanning haplotypes contain variants, including large differences in α-satellite DNA content, which may influence the fidelity and bias of chromosome transmission. The discovery of cenhaps creates new opportunities to investigate their contribution to phenotypic variation, especially in meiosis and mitosis, as well as to more incisively model the unexpectedly rich evolution of these challenging genomic regions.}, }
@article {pmid31222847, year = {2019}, author = {Ackermann, RR and Arnold, ML and Baiz, MD and Cahill, JA and Cortés-Ortiz, L and Evans, BJ and Grant, BR and Grant, PR and Hallgrimsson, B and Humphreys, RA and Jolly, CJ and Malukiewicz, J and Percival, CJ and Ritzman, TB and Roos, C and Roseman, CC and Schroeder, L and Smith, FH and Warren, KA and Wayne, RK and Zinner, D}, title = {Hybridization in human evolution: Insights from other organisms.}, journal = {Evolutionary anthropology}, volume = {28}, number = {4}, pages = {189-209}, pmid = {31222847}, issn = {1520-6505}, support = {T32 GM007544/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; Female ; Genome, Human/genetics ; *Hominidae/anatomy &amp; histology/genetics ; Humans ; Hybridization, Genetic/*genetics ; Male ; Mice ; Neanderthals/anatomy &amp; histology/genetics ; Phenotype ; Skull/anatomy &amp; histology ; }, abstract = {During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex-differences in behavior, Haldane's rule and the large X-effect, and transgressive phenotypic variation.}, }
@article {pmid31220106, year = {2019}, author = {Degano, I and Soriano, S and Villa, P and Pollarolo, L and Lucejko, JJ and Jacobs, Z and Douka, K and Vitagliano, S and Tozzi, C}, title = {Hafting of Middle Paleolithic tools in Latium (central Italy): New data from Fossellone and Sant'Agostino caves.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0213473}, pmid = {31220106}, issn = {1932-6203}, mesh = {Adhesives ; Animals ; Fires ; History, Ancient ; Hominidae ; *Neanderthals ; Resins, Plant ; Technology/*methods ; *Tool Use Behavior ; }, abstract = {Hafting of stone tools was an important advance in the technology of the Paleolithic. Evidence of hafting in the Middle Paleolithic is growing and is not limited to points hafted on spears for thrusting or throwing. This article describes the identification of adhesive used for hafting on a variety of stone tools from two Middle Paleolithic caves in Latium, Fossellone Cave and Sant'Agostino Cave. Analysis of the organic residue by gas chromatography/mass spectrometry shows that a conifer resin adhesive was used, in one case mixed with beeswax. Contrary to previous suggestions that the small Middle Paleolithic tools of Latium could be used by hand and that hafting was not needed since it did not improve their functionality, our evidence shows that hafting was used by Neandertals in central Italy. Ethnographic evidence indicates that resin, which dries when exposed to air, is generally warmed by exposure to a small fire thus softened to be molded and pushed in position in the haft. The use of resin at both sites suggests regular fire use, as confirmed by moderate frequencies of burnt lithics in both assemblages. Lithic analysis shows that hafting was applied to a variety of artifacts, irrespective of type, size and technology. Prior to our study evidence of hafting in the Middle Paleolithic of Italy was limited to one case only.}, }
@article {pmid31203846, year = {2019}, author = {Fiorenza, L and Benazzi, S and Kullmer, O and Zampirolo, G and Mazurier, A and Zanolli, C and Macchiarelli, R}, title = {Dental macrowear and cortical bone distribution of the Neanderthal mandible from Regourdou (Dordogne, Southwestern France).}, journal = {Journal of human evolution}, volume = {132}, number = {}, pages = {174-188}, doi = {10.1016/j.jhevol.2019.05.005}, pmid = {31203846}, issn = {1095-8606}, mesh = {Animals ; *Diet ; France ; Mandible/*anatomy &amp; histology ; *Mastication ; Neanderthals/*anatomy &amp; histology ; Tooth/*anatomy &amp; histology ; }, abstract = {Tooth wear is an important feature for reconstructing diet, food processing and cultural habits of past human populations. In particular, occlusal wear facets can be extremely useful for detecting information about diet and non-masticatory behaviors. The aim of this study is to reconstruct the diet and cultural behavior of the Neanderthal specimen Regourdou 1 (Dordogne, Southern France) from the analysis of the macrowear pattern, using the occlusal fingerprint analysis method. In addition, we have also examined whether there is any association between the observed dental macrowear and mandibular bone distribution and root dentine thickness. The posterior dentition of Regourdou 1 is characterized by an asymmetric wear pattern, with the right side significantly more worn than the left. In contrast, the left lower P3 shows a more advanced wear than the right premolar, with unusual semicircular enamel wear facets. The results from occlusal fingerprint analysis of this unique pattern suggest tooth-tool uses for daily task activities. Moreover, the left buccal aspect of the mandibular cortical bone is thicker than its right counterpart, and the left P3 has a thicker radicular dentine layer than its antimere. These results show a certain degree of asymmetry in cortical bone topography and dentine tissue that could be associated with the observed dental macrowear pattern. The molar macrowear pattern also suggests that Regourdou 1 had a mixed diet typical of those populations living in temperate deciduous woodlands and Mediterranean habitats, including animal and plant foods. Although this study is limited to one Neanderthal individual, future analyses based on a larger sample may further assist us to better understand the existing relationship between mandibular architecture, occlusal wear and the masticatory apparatus in humans.}, }
@article {pmid31203843, year = {2019}, author = {Galletta, L and Stephens, NB and Bardo, A and Kivell, TL and Marchi, D}, title = {Three-dimensional geometric morphometric analysis of the first metacarpal distal articular surface in humans, great apes and fossil hominins.}, journal = {Journal of human evolution}, volume = {132}, number = {}, pages = {119-136}, doi = {10.1016/j.jhevol.2019.04.008}, pmid = {31203843}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Biomechanical Phenomena ; *Hand Strength ; Hominidae/*anatomy &amp; histology ; Humans ; Metacarpal Bones/*anatomy &amp; histology/physiology ; Neanderthals/anatomy &amp; histology ; *Range of Motion, Articular ; }, abstract = {Understanding the manual abilities of fossil hominins has been a focus of palaeoanthropological research for decades. Of interest are the morphological characteristics of the thumb due to its fundamental role in manipulation, particularly that of the trapeziometacarpal joint. Considerably less attention has been given to the thumb metacarpophalangeal (MCP) joint, which plays a role in stabilizing the thumb during forceful grasps and precision pinching. In this study we use a three-dimensional geometric morphometric approach to quantify the shape of the first metacarpal head in extant hominids (Homo, Pan, Gorilla and Pongo) and six fossil hominin species (Homo neanderthalensis Tabun C1 and La Chappelle-aux-Saints, Homo naledi U.W. 101-1282, Australopithecus sediba MH2, Paranthropus robustus/early Homo SK84, Australopithecus africanus StW 418, Australopithecus afarensis A.L. 333w-39), with the aims of identifying shapes that may be correlated with human-like forceful opposition and determining if similar morphologies are present in fossil hominins. Results show that humans differ from extant great apes by having a distally flatter articular surface, larger epicondyle surface area, and a larger radial palmar condyle. We suggest that this suite of features is correlated with a lower range of motion at the MCP joint, which would enhance the thumbs ability to resist the elevated loads associated with the forceful precision grips typical of humans. Great ape genera are each differentiated by distinctive morphological features, each of which is consistently correlated with the predicted biomechanical demands of their particular locomotor and/or manipulatory habits. Neanderthals and U.W. 101-1282 fall within the modern human range of variation, StW 418, SK 84 and U.W. 88-119 fall in between humans and great apes, and A.L. 333w-39 falls within Pan variation. These results agree with those of traditional linear analyses while providing a more comprehensive quantitative basis from which to interpret the hand functional morphology of extinct hominins.}, }
@article {pmid31196864, year = {2019}, author = {Haber, M and Jones, AL and Connell, BA and Asan,  and Arciero, E and Yang, H and Thomas, MG and Xue, Y and Tyler-Smith, C}, title = {A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans Out of Africa.}, journal = {Genetics}, volume = {212}, number = {4}, pages = {1421-1428}, pmid = {31196864}, issn = {1943-2631}, support = {//Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Chromosomes, Human, Y/*genetics ; *Evolution, Molecular ; *Haplotypes ; *Human Migration ;